The tumor purity threshold analyses have not yet (all) made it to run-manuscript-analyses.sh, which is a problem if we're including it in generate-figures.sh since the model is to run run-manuscript-analyses.sh before generate-figures.sh.
To address this, we need to:
Make sure all tumor purity analyses that produce figures for the manuscript are run out of run-manuscript-analyses.sh. The modules with tumor purity to check here include:
From this comment: https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1678#pullrequestreview-1306452900
To address this, we need to:
Make sure all tumor purity analyses that produce figures for the manuscript are run out of
run-manuscript-analyses.sh. The modules with tumor purity to check here include:gene-set-enrichment-analysisimmune-deconvtelomerase-activity-predictiontp53_nf1_scoretranscriptomic-dimension-reductiontumor-purity-explorationDo another local run as follows:
Go ahead and update the
analyses/README.mdto indicate thattumor-purity-explorationis used in the MS.