Mercurial > repos > iuc > limma_voom
comparison limma_voom.R @ 16:5d903d528193 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 349e35a66009449851b21e2810bc5aaa58225fca
author | iuc |
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date | Sat, 09 Feb 2019 07:35:04 -0500 |
parents | 3133e833b3ce |
children | 86b3df7db58b |
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15:41573afd6871 | 16:5d903d528193 |
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835 downCount[i] <- sumStatus["Down", i] | 835 downCount[i] <- sumStatus["Down", i] |
836 flatCount[i] <- sumStatus["NotSig", i] | 836 flatCount[i] <- sumStatus["NotSig", i] |
837 | 837 |
838 # Write top expressions table | 838 # Write top expressions table |
839 if (wantTreat) { | 839 if (wantTreat) { |
840 top <- topTreat(fit, coef=i, number=Inf, sort.by="P") | 840 top <- topTreat(fit, coef=i, adjust.method=opt$pAdjOpt, number=Inf, sort.by="P") |
841 } else{ | 841 } else{ |
842 top <- topTable(fit, coef=i, number=Inf, sort.by="P") | 842 top <- topTable(fit, coef=i, adjust.method=opt$pAdjOpt, number=Inf, sort.by="P") |
843 } | 843 } |
844 write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE) | 844 write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE) |
845 linkName <- paste0(deMethod, "_", con, ".tsv") | 845 linkName <- paste0(deMethod, "_", con, ".tsv") |
846 linkAddr <- paste0(deMethod, "_", con, ".tsv") | 846 linkAddr <- paste0(deMethod, "_", con, ".tsv") |
847 linkData <- rbind(linkData, c(linkName, linkAddr)) | 847 linkData <- rbind(linkData, c(linkName, linkAddr)) |