Mercurial > repos > iuc > dexseq

comparison dexseq.R @ 5:28a2181df3b9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
author iuc
date Thu, 08 Oct 2015 16:49:40 -0400
parents 276833129f97
children 0ccbed58b270
comparison
equal deleted inserted replaced
4:7069d55968fb 5:28a2181df3b9
98 print("Results") 98 print("Results")
99 table(res$padj <= opt$fdr) 99 table(res$padj <= opt$fdr)
100 resSorted <- res[order(res$padj),] 100 resSorted <- res[order(res$padj),]
101 head(resSorted) 101 head(resSorted)
102 102
103 write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE) 103 export_table <- as.data.frame(resSorted)
104 last_column <- ncol(export_table)
105 for(i in 1:nrow(export_table)) {
106 export_table[i,last_column] <- paste(export_table[i,last_column][[1]],collapse=", ")
107 }
108 write.table(export_table, file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE)
104 print("Written Results") 109 print("Written Results")
105 110
106 if ( !is.null(opt$reportdir) ) { 111 if ( !is.null(opt$reportdir) ) {
107 save(dxd, resSorted, file = file.path(opt$reportdir,"DEXSeq_analysis.RData")) 112 save(dxd, resSorted, file = file.path(opt$reportdir,"DEXSeq_analysis.RData"))
108 save.image() 113 save.image()