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comparison deseq2.R @ 24:71bacea10eee 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 17:08:08 -0500
parents a6fc9228e1a0
children de44f8eff84a
comparison
equal deleted inserted replaced
23:0696db066a5b 24:71bacea10eee
352 independentFiltering=independentFiltering) 352 independentFiltering=independentFiltering)
353 resSorted <- res[order(res$padj),] 353 resSorted <- res[order(res$padj),]
354 outDF <- as.data.frame(resSorted) 354 outDF <- as.data.frame(resSorted)
355 outDF$geneID <- rownames(outDF) 355 outDF$geneID <- rownames(outDF)
356 outDF <- outDF[,c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")] 356 outDF <- outDF[,c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
357 filename <- paste0(opt$outfile,".",primaryFactor,"_",lvl,"_vs_",ref) 357 filename <- paste0(primaryFactor,"_",lvl,"_vs_",ref)
358 write.table(outDF, file=filename, sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE) 358 write.table(outDF, file=filename, sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)
359 if (independentFiltering) { 359 if (independentFiltering) {
360 threshold <- unname(attr(res, "filterThreshold")) 360 threshold <- unname(attr(res, "filterThreshold"))
361 } else { 361 } else {
362 threshold <- 0 362 threshold <- 0