Deprecate Selection Strategy Comparison (#589)

AlexsLemonade · Mar 2, 2020 · 0d9a85e · 0d9a85e
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diff --git 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
@@ -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` <br> `pbta-fusion-putative-oncogenic.tsv` <br> `analyses/focal-cn-file-preparation/results/controlfreec_annotated_cn_autosomes.tsv.gz` <br> `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` <br> `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` <br> `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` <br> `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` <br> `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` <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` <br> `results/consensus/pbta-snv-mutation-tmb.tsv` <br> `results/consensus/pbta-snv-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