From 0d9a85ea585f25bade2a62c5e54539270021d4dd Mon Sep 17 00:00:00 2001 From: jashapiro Date: Mon, 2 Mar 2020 13:40:21 -0500 Subject: [PATCH] Deprecate Selection Strategy Comparison (#589) --- .circleci/config.yml | 7 ++++--- analyses/README.md | 2 +- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 13c4ec307d..14224c9c80 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -76,9 +76,10 @@ jobs: name: Sex prediction from RNA-seq - Clean data-train elasticnet-evaluate model command: OPENPBTA_PERCENT=0 ./scripts/run_in_ci.sh bash analyses/sex-prediction-from-RNASeq/run-sex-prediction-from-RNASeq.sh - - run: - name: Selection Strategy Comparison - command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/selection-strategy-comparison/01-selection-strategies.rmd', params = list(neighbors = 2), clean = TRUE)" + # Deprecated: this comparison is no longer needed after separating Poly-A and stranded. + # - run: + # name: Selection Strategy Comparison + # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/selection-strategy-comparison/01-selection-strategies.rmd', params = list(neighbors = 2), clean = TRUE)" - run: name: TP53 NF1 classifier run diff --git a/analyses/README.md b/analyses/README.md index a510d0f00c..aaae9ac986 100644 --- a/analyses/README.md +++ b/analyses/README.md @@ -37,7 +37,7 @@ Note that _nearly all_ modules use the harmonized clinical data file (`pbta-hist | [`oncoprint-landscape`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/oncoprint-landscape) | `pbta-snv-consensus-mutation.maf.tsv.gz`
`pbta-fusion-putative-oncogenic.tsv`
`analyses/focal-cn-file-preparation/results/controlfreec_annotated_cn_autosomes.tsv.gz`
`independent-specimens.*` | Combines mutation, copy number, and fusion data into an OncoPrint plot ([#6](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/6)); will need to be updated as all data types are refined | N/A | [`run-gistic`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/run-gistic) | `pbta-histologies.tsv`
`pbta-cnv-consensus.seg.gz` | *In progress* Runs GISTIC 2.0 on SEG files | Currently N/A | [`sample-distribution-analysis`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/sample-distribution-analysis) | `pbta-histologies.tsv` | Produces plots and tables that illustrate the distribution of different histologies in the PBTA data | N/A -| [`selection-strategy-comparison`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/selection-strategy-comparison) | `pbta-gene-expression-rsem-fpkm.polya.rds`
`pbta-gene-expression-rsem-fpkm.stranded.rds` | Comparison of RNA-seq data from different selection strategies | N/A +| [`selection-strategy-comparison`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/selection-strategy-comparison) | `pbta-gene-expression-rsem-fpkm.polya.rds`
`pbta-gene-expression-rsem-fpkm.stranded.rds` | *Deprecated*; Comparison of RNA-seq data from different selection strategies | N/A | [`sex-prediction-from-RNASeq`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/sex-prediction-from-RNASeq) | `pbta-gene-expression-kallisto.stranded.rds`
`pbta-histologies.tsv` | *In progress*; predicts genetic sex using RNA-seq data ([#84](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/6)) | N/A | [`snv-callers`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/snv-callers) | `pbta-snv-lancet.vep.maf.gz`
`pbta-snv-mutect2.vep.maf.gz`
`pbta-snv-strelka2.vep.maf.gz`
`pbta-snv-vardict.vep.maf.gz`
`tcga-snv-lancet.vep.maf.gz`
`tcga-snv-mutect2.vep.maf.gz`
`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`
`results/consensus/pbta-snv-mutation-tmb.tsv`
`results/consensus/pbta-snv-mutation-tmb-coding.tsv`(included in data download; too large for tracking via GitHub)
`results/consensus/tcga-snv-consensus-mutation.maf.tsv.gz`
`results/consensus/tcga-snv-mutation-tmb.tsv`
`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