diff --git a/CHANGELOG.md b/CHANGELOG.md index 169ed7fed6b9891ea3c6698b914f89bcded6c99f..ee3ac2203267513b79b841638ae0f717e601b2aa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,8 +3,11 @@ * Output: * inputBag * outputBag +* Remove gene details from tpm table +* Add EntrezID translation to tpm table (from version specific reference) **Background** +* Add GeneSymbol/EnsemblID/EntrezID translation files to references *Known Bugs* * outputBag does not contain fetch for processed data diff --git a/docs/dag.png b/docs/dag.png index a360ca8992473d8414143fb38bf13bfb6f6d4cce..04aafa139a1715cdd8213ae7a81a25dfaf6b4dac 100755 Binary files a/docs/dag.png and b/docs/dag.png differ diff --git a/workflow/scripts/convertGeneSymbols.R b/workflow/scripts/convertGeneSymbols.R index 7b05b92e5d251050a78e7f546aa8b042d994c623..92d3c3e2e8ad97ebacbca3c5f9d0fc185ceafb7e 100644 --- a/workflow/scripts/convertGeneSymbols.R +++ b/workflow/scripts/convertGeneSymbols.R @@ -19,6 +19,6 @@ convert <- convert[,-1] colnames(convert) <- c("GeneID","EntrezID") convert <- unique(convert) -output <- merge(x=convert,y=countTable,by.x="GeneID",by.y="Geneid",all.x=TRUE) +output <- merge(x=convert,y=countTable[,c("Geneid","count","tpm")],by.x="GeneID",by.y="Geneid",all.x=TRUE) -write.table(output,file=paste0(opt$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE) \ No newline at end of file +write.table(output,file=paste0(opt$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE)