arichards2564
arichards2564
https://github.com/ExpressionAnalysis/STAR-SEQR/blob/8889bc879c647c2174c37ee4a69a27626814c22b/starseqr.py#L443-L446 I'm trying to use a pre-aligned bam and it errors here because it looks for sam file that doesn't exist. I believe this is a mistake. Do I need...
https://github.com/mskcc/facets-suite/blob/7d54d0f67e3136bd60d94ad810a9c855df113096/R/gene-level-changes.R#L45 While generally unlikely, if we're using the WGD derived from the segments from the hisens run, this could conflict with the overall call of WGD where we use the...
https://github.com/mskcc/facets-suite/blob/7d54d0f67e3136bd60d94ad810a9c855df113096/R/check-fit.R#L181 Is this supposed to be sum(X) as opposed to sum(length(X))?
https://github.com/mskcc/facets-suite/blob/7d54d0f67e3136bd60d94ad810a9c855df113096/R/plot-facets.R#L191
https://github.com/mskcc/facets-suite/blob/41a01fe9afb947f38af2802cf62189e0a1061cc5/R/ccf-annotate-maf.R#L58 Here, we overwrite the true read depth with alt+ref. Normally, this doesn't change much but I've seen positions where there are 3 alleles present at a given position and...
https://github.com/mskcc/facets-suite/blob/8a6e3712d8866f1bfb04729247b2f7dca74bd0b9/R/gene-level-changes.R#L111 This line and the next are incorrect. The filters for cf and number of genes on segment are only being applied when the amp is already too big. These...
https://github.com/mskcc/facets-suite/blob/b197695e0328bb81f778af53c3b9682b73c2dcba/annotate-maf-wrapper.R#L107 I'm not sure if it was the version of R but I was getting an error with this version: Error in rbindlist(output_maf, maf[!which(maf$Tumor_Sample_Barcode %in% : Input is data.table but...
I believe that p.value.log is actually referring to the log of the likelihood ratio test, whereas the p.value.sc is referring to the score log-rank test. According to this: https://rdrr.io/cran/survival/src/R/summary.coxph.R the...