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Remove lgg histone mut hgg subtyping (#851)
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* remove LGAT from HGG subtyping based on defining lesions

* change order of operations

add filtering at MAF step instead of later so that those samples are not captured in the final snv_lesions_df

* Update README.md

* update all files with module run

I added a note to the shell script about installing BEDOPS locally as a requirement for that code to run.
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Jo Lynne Rokita authored Nov 24, 2020
1 parent 4fa4c63 commit 0a6e543
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47 changes: 40 additions & 7 deletions analyses/molecular-subtyping-HGG/01-HGG-molecular-subtyping-defining-lesions.Rmd
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Expand Up @@ -23,6 +23,8 @@ Rscript -e "rmarkdown::render('analyses/molecular-subtyping-HGG/01-HGG-molecular
# Set Up

```{r}
library(tidyverse)
# Get `magrittr` pipe
`%>%` <- dplyr::`%>%`
```
Expand All @@ -35,6 +37,12 @@ Rscript -e "rmarkdown::render('analyses/molecular-subtyping-HGG/01-HGG-molecular
# matter where this is called from
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
# Get lgat subset folder from the module in master
lgat_subset_dir <- file.path(root_dir,
"analyses",
"molecular-subtyping-LGAT",
"lgat-subset")
# File path to results directory
results_dir <-
file.path(root_dir, "analyses", "molecular-subtyping-HGG", "results")
Expand All @@ -49,19 +57,44 @@ metadata <-
guess_max = 10000) %>%
dplyr::filter(sample_type == "Tumor")
# Read in snv consensus mutation data
# File from 00-LGAT-select-pathology-dx that is used for inclusion/exclusion
path_dx_list_lgat <- jsonlite::fromJSON(
file.path(lgat_subset_dir,
"lgat_subtyping_path_dx_strings.json")
)
```

# Prepare Data

```{r}
# Get LGAT tumor samples on the basis of pathology diagnosis
lgat_specimens <- metadata %>%
filter(str_detect(str_to_lower(pathology_diagnosis), # Inclusion criteria
paste0(path_dx_list_lgat$include_path_dx, collapse = "|")),
# Exclusion criteria
str_detect(str_to_lower(pathology_diagnosis),
paste0(path_dx_list_lgat$exclude_path_dx, collapse = "|"),
negate = TRUE),
# Tumors
sample_type == "Tumor",
composition == "Solid Tissue") %>%
pull(Kids_First_Biospecimen_ID)
```

# Read in snv consensus mutation data, filtering out LGAT
```{r}
snv_df <-
data.table::fread(file.path(root_dir,
"data",
"pbta-snv-consensus-mutation.maf.tsv.gz"))
"pbta-snv-consensus-mutation.maf.tsv.gz")) %>%
filter(!Tumor_Sample_Barcode %in% lgat_specimens)
```

# Prepare Data

## SNV consensus mutation data - defining lesions

```{r}
# Filter the snv consensus mutatation data for the target lesions
# Filter the snv consensus mutation data for the target lesions
snv_lesions_df <- snv_df %>%
dplyr::filter(Hugo_Symbol %in% c("H3F3A", "HIST1H3B",
"HIST1H3C", "HIST2H3C") &
Expand Down Expand Up @@ -91,9 +124,9 @@ snv_lesions_df <- snv_df %>%
dplyr::select(
-HGVSp_Short,
-Hugo_Symbol
)
)
# add back in samples with no evidence of these specific mutations
# add back in samples with no evidence of these specific mutations and are not LGAT
snv_lesions_df <- snv_lesions_df %>%
dplyr::bind_rows(
data.frame(
Expand Down Expand Up @@ -148,4 +181,4 @@ readr::write_tsv(snv_lesions_df,
```{r}
# Print the session information
sessionInfo()
```
```
239 changes: 151 additions & 88 deletions analyses/molecular-subtyping-HGG/01-HGG-molecular-subtyping-defining-lesions.nb.html
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163 changes: 83 additions & 80 deletions analyses/molecular-subtyping-HGG/03-HGG-molecular-subtyping-cnv.nb.html
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Expand Up @@ -7,6 +7,7 @@
<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />


<meta name="author" content="Chante Bethell, Stephanie J. Spielman, and Jaclyn Taroni for ALSF CCDL" />
Expand Down Expand Up @@ -2559,7 +2560,7 @@

// create a collapsable div to wrap the code in
var div = $('<div class="collapse r-code-collapse"></div>');
if (show)
if (show || $(this)[0].classList.contains('fold-show'))
div.addClass('in');
var id = 'rcode-643E0F36' + currentIndex++;
div.attr('id', id);
Expand Down Expand Up @@ -2689,7 +2690,6 @@
}
img {
max-width:100%;
height: auto;
}
.tabbed-pane {
padding-top: 12px;
Expand Down Expand Up @@ -2787,58 +2787,13 @@
}
</style>

<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});

$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
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});
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<!-- code folding -->
<style type="text/css">
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</style>
<script>
$(document).ready(function () {
window.initializeSourceEmbed("03-HGG-molecular-subtyping-cnv.Rmd");
window.initializeCodeFolding("show" === "show");
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<script>
$(document).ready(function () {

// move toc-ignore selectors from section div to header
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#TOC {
Expand Down Expand Up @@ -2943,7 +2898,7 @@ <h4 class="date">2020</h4>
<div id="usage" class="section level2">
<h2>Usage</h2>
<p>This notebook is intended to be run via the command line from the top directory of the repository as follows:</p>
<p><code>Rscript -e &quot;rmarkdown::render('analyses/molecular-subtyping-HGG/03-HGG-molecular-subtyping-cnv.Rmd', clean = TRUE)&quot;</code></p>
<p><code>Rscript -e &quot;rmarkdown::render(&#39;analyses/molecular-subtyping-HGG/03-HGG-molecular-subtyping-cnv.Rmd&#39;, clean = TRUE)&quot;</code></p>
</div>
<div id="set-up" class="section level2">
<h2>Set Up</h2>
Expand All @@ -2955,12 +2910,15 @@ <h2>Set Up</h2>
<!-- rnb-message-begin eyJkYXRhIjoi4pSA4pSAIEF0dGFjaGluZyBwYWNrYWdlcyDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIAgdGlkeXZlcnNlIDEuMi4xIOKUgOKUgFxuIn0= -->
<pre><code>── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──</code></pre>
<!-- rnb-message-end -->
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<pre><code>✔ ggplot2 3.2.0 ✔ purrr 0.3.2
✔ tibble 2.1.3 ✔ dplyr 0.8.3
✔ tidyr 0.8.3 ✔ stringr 1.4.0
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<pre><code>✔ ggplot2 3.2.1 ✔ purrr 0.3.3
✔ tibble 3.0.3 ✔ dplyr 0.8.3
✔ tidyr 1.0.0 ✔ stringr 1.4.0
✔ readr 1.3.1 ✔ forcats 0.4.0</code></pre>
<!-- rnb-message-end -->
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<pre><code>Warning: package &#39;tibble&#39; was built under R version 3.6.2</code></pre>
<!-- rnb-warning-end -->
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<pre><code>── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
Expand Down Expand Up @@ -3061,7 +3019,7 @@ <h4>Inclusion Criteria</h4>
<!-- rnb-output-end -->
<!-- rnb-chunk-end -->
<!-- rnb-text-begin -->
<p>We’d then expect 142 samples to have non-NA values in the cleaned CNV files.</p>
<p>We’d then expect 141 samples to have non-NA values in the cleaned CNV files.</p>
</div>
<div id="read-in-cn-data" class="section level4">
<h4>Read in CN Data</h4>
Expand Down Expand Up @@ -3233,8 +3191,8 @@ <h2>Join Together</h2>
<!-- rnb-source-begin eyJkYXRhIjoibnJvdyhmaW5hbF9oZ2dfY25fZGYpIn0= -->
<pre class="r"><code>nrow(final_hgg_cn_df)</code></pre>
<!-- rnb-source-end -->
<!-- rnb-output-begin eyJkYXRhIjoiWzFdIDE0MlxuIn0= -->
<pre><code>[1] 142</code></pre>
<!-- rnb-output-begin eyJkYXRhIjoiWzFdIDE0MVxuIn0= -->
<pre><code>[1] 141</code></pre>
<!-- rnb-output-end -->
<!-- rnb-chunk-end -->
<!-- rnb-text-begin -->
Expand Down Expand Up @@ -3264,43 +3222,39 @@ <h2>Session Info</h2>
<!-- rnb-source-begin eyJkYXRhIjoic2Vzc2lvbkluZm8oKSJ9 -->
<pre class="r"><code>sessionInfo()</code></pre>
<!-- rnb-source-end -->
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<pre><code>R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
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<pre><code>R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3 purrr_0.3.2
[5] readr_1.3.1 tidyr_0.8.3 tibble_2.1.3 ggplot2_3.2.0
[1] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3 purrr_0.3.3
[5] readr_1.3.1 tidyr_1.0.0 tibble_3.0.3 ggplot2_3.2.1
[9] tidyverse_1.2.1

loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 cellranger_1.1.0 pillar_1.4.2 compiler_3.6.0
[5] base64enc_0.1-3 tools_3.6.0 digest_0.6.20 lubridate_1.7.4
[9] jsonlite_1.6 evaluate_0.14 nlme_3.1-140 gtable_0.3.0
[13] lattice_0.20-38 pkgconfig_2.0.2 rlang_0.4.0 cli_1.1.0
[17] rstudioapi_0.10 yaml_2.2.0 haven_2.1.1 xfun_0.8
[21] withr_2.1.2 xml2_1.2.0 httr_1.4.0 knitr_1.23
[25] generics_0.0.2 hms_0.4.2 rprojroot_1.3-2 grid_3.6.0
[29] tidyselect_0.2.5 glue_1.3.1 R6_2.4.0 readxl_1.3.1
[33] rmarkdown_1.13 modelr_0.1.4 magrittr_1.5 backports_1.1.4
[37] scales_1.0.0 htmltools_0.3.6 rvest_0.3.4 assertthat_0.2.1
[41] colorspace_1.4-1 stringi_1.4.3 lazyeval_0.2.2 munsell_0.5.0
[45] broom_0.5.2 crayon_1.3.4 </code></pre>
[1] Rcpp_1.0.5 cellranger_1.1.0 pillar_1.4.6 compiler_3.6.1
[5] base64enc_0.1-3 tools_3.6.1 digest_0.6.22 lubridate_1.7.4
[9] jsonlite_1.6 evaluate_0.14 lifecycle_0.2.0 gtable_0.3.0
[13] pkgconfig_2.0.3 rlang_0.4.7 cli_1.1.0 rstudioapi_0.10
[17] yaml_2.2.0 haven_2.1.1 xfun_0.10 withr_2.1.2
[21] xml2_1.2.2 httr_1.4.1 knitr_1.25 generics_0.0.2
[25] vctrs_0.3.2 hms_0.5.1 rprojroot_1.3-2 grid_3.6.1
[29] tidyselect_1.1.0 glue_1.3.1 R6_2.4.0 readxl_1.3.1
[33] rmarkdown_1.16 modelr_0.1.5 magrittr_1.5 backports_1.1.5
[37] scales_1.0.0 ellipsis_0.3.0 htmltools_0.4.0 rvest_0.3.4
[41] assertthat_0.2.1 colorspace_1.4-1 stringi_1.4.3 lazyeval_0.2.2
[45] munsell_0.5.0 broom_0.7.0 crayon_1.3.4 </code></pre>
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