Merge branch 'devel' of https://github.com/lima1/PureCN into devel

lima1 · May 12, 2024 · 9080c51 · 9080c51
2 parents 7905ce8 + 476f205
commit 9080c51
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: PureCN
 Type: Package
 Title: Copy number calling and SNV classification using
     targeted short read sequencing
-Version: 2.11.0
-Date: 2024-04-24
+Version: 2.11.1
+Date: 2024-05-10
 Authors@R: c(person("Markus", "Riester",
                     role = c("aut", "cre"),
                     email = "markus.riester@novartis.com",

diff --git a/NEWS b/NEWS
@@ -1,3 +1,14 @@
+Changes in version 2.12.0
+-------------------------
+
+NEW FEATURES
+
+    o Added --num-eigen-vectors to PureCN.R to set the number of eigen vectors.
+      Tuning parameter for coverage normalization. Default should in most cases
+      be a good compromise between removing most normal noise and not
+      overfitting to pool of normal samples.
+
+
 Changes in version 2.10.0
 -------------------------
 

diff --git a/README.md b/README.md
@@ -31,7 +31,7 @@ For outdated R/Bioconductor versions, you can try backporting the latest stable
 version (this should work fine for Bioconductor 3.3 and later):
 
 ```
-BiocManager::install("lima1/PureCN", ref = "RELEASE_3_18")
+BiocManager::install("lima1/PureCN", ref = "RELEASE_3_19")
 ```
 
 If you want the latest and greatest from the developer branch:

diff --git a/inst/extdata/PureCN.R b/inst/extdata/PureCN.R
@@ -71,6 +71,9 @@ option_list <- list(
     make_option(c("--min-fraction-offtarget"), action = "store", type = "double",
         default = formals(PureCN::filterIntervals)$min.fraction.offtarget,
         help = "Interval Filter: Ignore off-target internals when only the specified fraction of all intervals are off-target intervals  [default %default]"),
+    make_option(c("--num-eigen-vectors"), action = "store", type = "integer",
+        default = formals(PureCN::calculateTangentNormal)$num.eigen,
+        help = "Coverage Normalization: Number of eigen vectors when --normaldb is provided [default %default]"),
     make_option(c("--fun-segmentation"), action = "store", type = "character", default = "CBS",
         help = "Segmentation: Algorithm. CBS, PSCBS, GATK4, Hclust, or none [default %default]"),
     make_option(c("--alpha"), action = "store", type = "double",
@@ -283,7 +286,7 @@ if (file.exists(file.rds) && !opt$force) {
         if (!is.null(normalDB)) {
             if (is.null(normal.coverage.file)) {
                 normal.coverage.file <- calculateTangentNormal(tumor.coverage.file,
-                    normalDB)
+                    normalDB, num.eigen = opt[["num_eigen_vectors"]])
             }
         } else if (is.null(normal.coverage.file) && is.null(seg.file) &&
                    is.null(log.ratio)) {