Rename module: sv-analysis -> chromothripsis

.circleci/config.yml

@@ -182,7 +182,7 @@ jobs:
 
       - run:
           name: Process SV file
-          command: ./scripts/run_in_ci.sh Rscript analyses/sv-analysis/01-process-sv-file.R
+          command: ./scripts/run_in_ci.sh Rscript analyses/chromothripsis/01-process-sv-file.R
 
 #      - run:
 #          name: Oncoprint plotting
@@ -206,7 +206,7 @@ jobs:
 
       - run:
           name: Add Shatterseek
-          command: ./scripts/run_in_ci.sh Rscript analyses/sv-analysis/02-shatterseek.R
+          command: ./scripts/run_in_ci.sh Rscript analyses/chromothripsis/02-shatterseek.R
 
       - run:
           name: Telomerase activity

analyses/README.md

@@ -12,6 +12,7 @@ Note that _nearly all_ modules use the harmonized clinical data file (`pbta-hist
 | Module | Input Files | Brief Description | Output Files Consumed by Other Analyses |
 |--------|-------|-------------------|--------------|
 | [`chromosomal-instability`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/chromosomal-instability) | `pbta-histologies.tsv` <br> `pbta-sv-manta.tsv.gz` <br> `pbta-cnv-cnvkit.seg.gz` | Evaluates chromosomal instability by calculating chromosomal breakpoint densities and by creating circular plot visuals | N/A
+| [`chromothripsis`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/chromothripsis) | `pbta-sv-manta.tsv.gz` <br> `pbta-cnv-consensus.seg.gz` <br> `independent-specimens.wgs.primary-plus.tsv` | *In progress*; chromothripsis analysis per [#1007](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1007)| N/A
 | [`cnv-chrom-plot`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/cnv-chrom) | `pbta-cnv-consensus-gistic.zip` <br> `analyses/copy_number_consensus_call/results/pbta-cnv-consensus.seg` | Plots genome wide visualizations relating to copy number results | N/A
 | [`cnv-comparison`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/cnv-comparison) | Earlier version of SEG files | *Deprecated*; compared earlier version of the CNV methods. | N/A
 | [`collapse-rnaseq`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/collapse-rnaseq) | `pbta-gene-expression-rsem-fpkm.polya.rds` <br> `pbta-gene-expression-rsem-fpkm.stranded.rds` <br> `gencode.v27.primary_assembly.annotation.gtf.gz` | Collapses RSEM FPKM matrices such that gene symbols are de-duplicated. | `results/pbta-gene-expression-rsem-fpkm-collapsed.polya.rds` (included in data download; too large for tracking via GitHub) <br> `results/pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` (included in data download; too large for tracking via GitHub)
@@ -51,7 +52,6 @@ Note that _nearly all_ modules use the harmonized clinical data file (`pbta-hist
 | [`snv-callers`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/snv-callers) | `pbta-snv-lancet.vep.maf.gz` <br> `pbta-snv-mutect2.vep.maf.gz` <br> `pbta-snv-strelka2.vep.maf.gz` <br> `pbta-snv-vardict.vep.maf.gz` <br> `tcga-snv-lancet.vep.maf.gz` <br> `tcga-snv-mutect2.vep.maf.gz` <br> `tcga-snv-strelka2.vep.maf.gz` | Generates consensus SNV and indel calls for PBTA and TCGA data; calculates tumor mutation burden using the consensus calls | `results/consensus/pbta-snv-consensus-mutation.maf.tsv.gz` (included in data download; too large for tracking via GitHub) <br> `results/consensus/pbta-snv-consensus-mutation-tmb-all.tsv` <br> `results/consensus/pbta-snv-consensus-mutation-tmb-coding.tsv`(included in data download; too large for tracking via GitHub) <br> `results/consensus/tcga-snv-consensus-mutation.maf.tsv.gz` <br> `results/consensus/tcga-snv-mutation-tmb.tsv` <br> `results/consensus/tcga-snv-mutation-tmb-coding.tsv`
 | [`ssgsea-hallmark`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/ssgsea-hallmark) | `pbta-gene-counts-rsem-expected_count.stranded.rds` | *Deprecated*; performs GSVA using Hallmark gene sets | N/A
 | [`survival-analysis`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/survival-analysis) | TBD | *In progress*; will eventually contain functions for various types of survival analysis ([#18](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/18)) | N/A
-| [`sv-analysis`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/sv-analysis) | `pbta-sv-manta.tsv.gz` <br> `independent-specimens.wgs.primary-plus.tsv` | *In progress*; chromothripsis analysis per [#27](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/27)| N/A
 | [`telomerase-activity-prediction`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/telomerase-activity-prediction)| `pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` <br> `pbta-gene-expression-rsem-fpkm-collapsed.polya.rds	` <br> `pbta-gene-counts-rsem-expected_count.stranded.rds` <br> `pbta-gene-counts-rsem-expected_count.polya.rds` | Quantify telomerase activity across pediatric brain tumors (part of [#148](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/148)) | `results/TelomeraseScores_PTBAPolya_counts` <br> `results/TelomeraseScores_PTBAPolya_FPKM.txt` <br> `results/TelomeraseScores_PTBAStranded_counts.txt` <br> `results/TelomeraseScores_PTBAStranded_FPKM.txt`
 | [`tmb-compare`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/tmb-compare) | `pbta-snv-consensus-mutation-tmb-coding.tsv` | Compares PBTA tumor mutation burden to adult TCGA data. The D3B TMB calculations (`TMB_d3b_code`) and its comparison notebook (`compare-tmb-calculations.Rmd`) are *deprecated*. | N/A
 | [`tp53_nf1_score`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/tp53_nf1_score) | `pbta-snv-consensus-mutation.maf.tsv.gz` <br> `pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` <br> `pbta-gene-expression-rsem-fpkm-collapsed.polya.rds` | Applies _TP53_ inactivation, _NF1_ inactivation, and Ras activation classifiers to RNA-seq data [#165](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/165)| N/A

analyses/chromothripsis/README.md

@@ -0,0 +1,19 @@
+## Chromothripsis Analysis (in progress)
+
+**Module authors :**
+Yang Yang ([@yangyangclover](https://github.com/yangyangclover))
+Modifications in progress by Laura Egolf ([@LauraEgolf](https://github.com/LauraEgolf/))
+
+This module runs ShatterSeek, classifies chromothripsis regions, and visualizes the results.
+
+#### Inputs from data download
+* independent-specimens.wgs.primary-plus.tsv
+* pbta-sv-manta.tsv
+* pbta-cnv-consensus.seg
+
+#### Order of scripts in analysis
+`01-process-sv-file.R` : This script reformats SV files for ShatterSeek input.
+
+`02-shatterseek.R` : This script runs ShatterSeek and classifies chromothripsis regions as high or low confidence based on criteria recommended by the authors. [Modifications ongoing]
+
+More scripts will be added.