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Update HGG subtyping (4/11) #108

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merged 10 commits into from
Oct 28, 2024
Merged

Update HGG subtyping (4/11) #108

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eab63e8
update HGG subtyping module
komalsrathi Jun 20, 2024
96f6848
cancer_group_short is HGG where molecular_subtype is PXA
komalsrathi Aug 16, 2024
8e5bf85
Merge branch 'master' into update-subtyping
naqvia Aug 16, 2024
0f42796
rerun
komalsrathi Aug 19, 2024
11f2753
rerun with fread fix
komalsrathi Aug 19, 2024
6b901e8
Merge remote-tracking branch 'origin/master' into update-subtyping
komalsrathi Aug 20, 2024
8e69b0a
add txdbmaker
komalsrathi Aug 20, 2024
51c1f93
Merge pull request #118 from d3b-center/update-dockerfile
komalsrathi Aug 21, 2024
8e4f096
Merge pull request #106 from d3b-center/update-nf1-score
komalsrathi Oct 28, 2024
c48d996
Merge remote-tracking branch 'origin/master' into update-subtyping
komalsrathi Oct 28, 2024
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1 change: 1 addition & 0 deletions Dockerfile
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Expand Up @@ -53,6 +53,7 @@ RUN R -e 'BiocManager::install(c( \
"survival", \
"survminer", \
"sva", \
"txdbmaker", \
"WGCNA" \
))'

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71 changes: 37 additions & 34 deletions analyses/molecular-subtyping-HGG/00-fusion-summary.nb.html
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4 changes: 3 additions & 1 deletion analyses/molecular-subtyping-HGG/01-HOPE-HGG-subtyping-subset-file.Rmd
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Expand Up @@ -14,7 +14,7 @@ library(annoFuseData)

```{r directories}
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))

scratch_dir <- file.path(root_dir, "scratch")
analyses_dir <- hgg_subset_dir <- file.path(root_dir,
"analyses",
"molecular-subtyping-HGG")
Expand Down Expand Up @@ -59,10 +59,12 @@ keep_cols <- c("Chromosome",
# snv files
snv_tumor_maf <- data.table::fread(
file.path(root_dir, "data" , "Hope-tumor-only-snv-mutect2.maf.tsv.gz"),
tmpdir = scratch_dir,
select = keep_cols)

snv_consensus_hotspot_maf <- data.table::fread(
file.path(root_dir, "data" , "Hope-snv-consensus-plus-hotspots.maf.tsv.gz"),
tmpdir = scratch_dir,
select = keep_cols) %>%
bind_rows(snv_tumor_maf)

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95 changes: 50 additions & 45 deletions analyses/molecular-subtyping-HGG/01-HOPE-HGG-subtyping-subset-file.html
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Expand Up @@ -356,21 +356,21 @@ <h4 class="date">2023-08-02</h4>


<pre class="r"><code>library(tidyverse)</code></pre>
<pre><code>## ── Attaching core tidyverse packages ───────────────────────────────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.1.1 ✔ readr 2.1.4
## ✔ forcats 1.0.0 ✔ stringr 1.5.0
## ✔ ggplot2 3.4.2 ✔ tibble 3.2.1
## ✔ lubridate 1.9.2 ✔ tidyr 1.3.0
## ✔ purrr 1.0.1
## ── Conflicts ─────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
<pre><code>## ── Attaching core tidyverse packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.1.4 ✔ readr 2.1.5
## ✔ forcats 1.0.0 ✔ stringr 1.5.1
## ✔ ggplot2 3.5.1 ✔ tibble 3.2.1
## ✔ lubridate 1.9.3 ✔ tidyr 1.3.1
## ✔ purrr 1.0.2
## ── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
## ℹ Use the conflicted package (&lt;http://conflicted.r-lib.org/&gt;) to force all conflicts to become errors</code></pre>
<pre class="r"><code>library(annoFuseData)</code></pre>
<div id="get-directories" class="section level2">
<h2>Get directories</h2>
<pre class="r"><code>root_dir &lt;- rprojroot::find_root(rprojroot::has_dir(&quot;.git&quot;))

scratch_dir &lt;- file.path(root_dir, &quot;scratch&quot;)
analyses_dir &lt;- hgg_subset_dir &lt;- file.path(root_dir,
&quot;analyses&quot;,
&quot;molecular-subtyping-HGG&quot;)
Expand All @@ -388,8 +388,8 @@ <h2>Get directories</h2>
</div>
<div id="load-histologies-files" class="section level2">
<h2>load histologies files</h2>
<pre><code>## Rows: 634 Columns: 94
## ── Column specification ─────────────────────────────────────────────────────────────────────────────────
<pre><code>## Rows: 632 Columns: 94
## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## Delimiter: &quot;\t&quot;
## chr (56): Kids_First_Biospecimen_ID, sample_id, Kids_First_Participant_ID, e...
## dbl (29): aliquot_id, age_at_diagnosis_days, age_at_event_days, age_at_chemo...
Expand All @@ -416,10 +416,12 @@ <h2>Defining lesions snv data</h2>
# snv files
snv_tumor_maf &lt;- data.table::fread(
file.path(root_dir, &quot;data&quot; , &quot;Hope-tumor-only-snv-mutect2.maf.tsv.gz&quot;),
tmpdir = scratch_dir,
select = keep_cols)

snv_consensus_hotspot_maf &lt;- data.table::fread(
file.path(root_dir, &quot;data&quot; , &quot;Hope-snv-consensus-plus-hotspots.maf.tsv.gz&quot;),
tmpdir = scratch_dir,
select = keep_cols) %&gt;%
bind_rows(snv_tumor_maf)

Expand Down Expand Up @@ -537,15 +539,15 @@ <h2>cn data</h2>
replace(is.na(.), &quot;Neutral&quot;) %&gt;%
distinct() %&gt;%
write_tsv(file.path(results_dir, &quot;HGG_cleaned_cnv.tsv&quot;))</code></pre>
<pre><code>## `summarise()` has grouped output by &#39;Kids_First_Biospecimen_ID&#39;. You can override using the `.groups`
## argument.</code></pre>
<pre><code>## `summarise()` has grouped output by &#39;Kids_First_Biospecimen_ID&#39;. You can
## override using the `.groups` argument.</code></pre>
</div>
<div id="mutations" class="section level2">
<h2>mutations</h2>
<pre class="r"><code>gencode_cds_bed &lt;- readr::read_tsv(file.path(root_dir, &quot;scratch&quot;, &quot;gencode.v39.primary_assembly.annotation.bed&quot;),
col_names = FALSE)</code></pre>
<pre><code>## Rows: 840001 Columns: 10
## ── Column specification ─────────────────────────────────────────────────────────────────────────────────
## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## Delimiter: &quot;\t&quot;
## chr (7): X1, X4, X5, X6, X7, X8, X10
## dbl (3): X2, X3, X9
Expand All @@ -555,7 +557,7 @@ <h2>mutations</h2>
<pre class="r"><code>defining_lesions_df &lt;- readr::read_tsv(file.path(results_dir, &quot;Hope_HGG_defining_lesions.tsv&quot;)) %&gt;%
rename(Tumor_Sample_Barcode = Kids_First_Biospecimen_ID)</code></pre>
<pre><code>## Rows: 110 Columns: 14
## ── Column specification ─────────────────────────────────────────────────────────────────────────────────
## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## Delimiter: &quot;\t&quot;
## chr (13): Kids_First_Participant_ID, sample_id, Kids_First_Biospecimen_ID, H...
## lgl (1): defining_lesion
Expand Down Expand Up @@ -680,11 +682,11 @@ <h1>Combine all together and save</h1>
<div id="fusion-subsetting" class="section level2">
<h2>fusion subsetting</h2>
<pre class="r"><code>fusion_hgg &lt;- read_tsv(file.path(analyses_dir, &quot;input&quot;, &quot;fusion_summary_hgg_foi.tsv&quot;)) </code></pre>
<pre><code>## Rows: 87 Columns: 35
## ── Column specification ─────────────────────────────────────────────────────────────────────────────────
<pre><code>## Rows: 87 Columns: 36
## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## Delimiter: &quot;\t&quot;
## chr (1): Kids_First_Biospecimen_ID
## dbl (34): BCL11A--ALK, BRAF--BRAF, CCDC88A--ALK, CHD7--MYBL1, CLIP1--ROS1, E...
## dbl (35): BCL11A--ALK, BRAF--BRAF, BRAF--WSB1, CCDC88A--ALK, CHD7--MYBL1, CL...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.</code></pre>
Expand Down Expand Up @@ -773,13 +775,13 @@ <h3>Clean and Wrangle Expression Data</h3>
clean_wrangle_expression(expression_matrix,
output_file_path = file.path(results_dir, &quot;HGG_cleaned_expression.tsv&quot;))</code></pre>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>## R version 4.2.3 (2023-03-15)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
<pre><code>## R version 4.4.0 (2024-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
Expand All @@ -789,35 +791,38 @@ <h3>Clean and Wrangle Expression Data</h3>
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] annoFuseData_0.1.0 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
## [5] dplyr_1.1.1 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0
## [9] tibble_3.2.1 ggplot2_3.4.2 tidyverse_2.0.0
## [1] annoFuseData_0.1.0 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
## [5] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1
## [9] tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.0 xfun_0.38 bslib_0.4.2
## [4] colorspace_2.1-0 vctrs_0.6.2 generics_0.1.3
## [7] htmltools_0.5.5 stats4_4.2.3 yaml_2.3.7
## [10] utf8_1.2.3 rlang_1.1.0 R.oo_1.25.0
## [13] jquerylib_0.1.4 pillar_1.9.0 glue_1.6.2
## [16] withr_2.5.0 R.utils_2.12.2 BiocGenerics_0.44.0
## [19] bit64_4.0.5 GenomeInfoDbData_1.2.9 lifecycle_1.0.3
## [22] zlibbioc_1.44.0 munsell_0.5.0 gtable_0.3.3
## [25] R.methodsS3_1.8.2 evaluate_0.20 knitr_1.42
## [28] IRanges_2.32.0 tzdb_0.3.0 fastmap_1.1.1
## [31] GenomeInfoDb_1.34.9 parallel_4.2.3 fansi_1.0.4
## [34] scales_1.2.1 cachem_1.0.7 S4Vectors_0.36.2
## [37] XVector_0.38.0 vroom_1.6.1 jsonlite_1.8.4
## [40] bit_4.0.5 hms_1.1.3 digest_0.6.31
## [43] stringi_1.7.12 GenomicRanges_1.50.2 grid_4.2.3
## [46] rprojroot_2.0.3 bitops_1.0-7 cli_3.6.1
## [49] tools_4.2.3 magrittr_2.0.3 sass_0.4.5
## [52] RCurl_1.98-1.12 crayon_1.5.2 pkgconfig_2.0.3
## [55] data.table_1.14.8 timechange_0.2.0 rmarkdown_2.21
## [58] R6_2.5.1 compiler_4.2.3</code></pre>
## [1] sass_0.4.9 utf8_1.2.4 generics_0.1.3
## [4] stringi_1.8.4 hms_1.1.3 digest_0.6.35
## [7] magrittr_2.0.3 evaluate_0.24.0 grid_4.4.0
## [10] timechange_0.3.0 fastmap_1.2.0 R.oo_1.26.0
## [13] rprojroot_2.0.4 jsonlite_1.8.8 R.utils_2.12.3
## [16] GenomeInfoDb_1.40.1 httr_1.4.7 fansi_1.0.6
## [19] UCSC.utils_1.0.0 scales_1.3.0 jquerylib_0.1.4
## [22] cli_3.6.2 rlang_1.1.4 crayon_1.5.2
## [25] XVector_0.44.0 R.methodsS3_1.8.2 bit64_4.0.5
## [28] munsell_0.5.1 withr_3.0.0 cachem_1.1.0
## [31] yaml_2.3.8 tools_4.4.0 parallel_4.4.0
## [34] tzdb_0.4.0 colorspace_2.1-0 GenomeInfoDbData_1.2.12
## [37] BiocGenerics_0.50.0 vctrs_0.6.5 R6_2.5.1
## [40] stats4_4.4.0 lifecycle_1.0.4 zlibbioc_1.50.0
## [43] IRanges_2.38.0 S4Vectors_0.42.0 bit_4.0.5
## [46] vroom_1.6.5 pkgconfig_2.0.3 pillar_1.9.0
## [49] bslib_0.7.0 gtable_0.3.5 glue_1.7.0
## [52] data.table_1.15.4 GenomicRanges_1.56.1 xfun_0.44
## [55] tidyselect_1.2.1 knitr_1.47 htmltools_0.5.8.1
## [58] rmarkdown_2.27 compiler_4.4.0</code></pre>
</div>
</div>
</div>
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