Mercurial > repos > iuc > deseq2

diff deseq2.R @ 36:d9f48120c02b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
author iuc
date Sat, 29 Feb 2020 22:07:45 +0000
parents 4f497a8a72e8
children 951876579237
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--- a/deseq2.R	Tue Mar 26 06:23:43 2019 -0400
+++ b/deseq2.R	Sat Feb 29 22:07:45 2020 +0000
@@ -354,7 +354,7 @@
       outDF <- as.data.frame(resSorted)
       outDF$geneID <- rownames(outDF)
       outDF <- outDF[,c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
-      filename <- paste0(opt$outfile,".",primaryFactor,"_",lvl,"_vs_",ref)
+      filename <- paste0(primaryFactor,"_",lvl,"_vs_",ref)
       write.table(outDF, file=filename, sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)
       if (independentFiltering) {
         threshold <- unname(attr(res, "filterThreshold"))