Mercurial > repos > iuc > edger
comparison edger.R @ 6:555659de7321 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629
| author | iuc |
|---|---|
| date | Sat, 09 Feb 2019 07:20:20 -0500 |
| parents | fb9b9f0f2f06 |
| children | 3d89af8a44f0 |
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| 5:fb9b9f0f2f06 | 6:555659de7321 |
|---|---|
| 524 upCount[i] <- sumStatus["Up", ] | 524 upCount[i] <- sumStatus["Up", ] |
| 525 downCount[i] <- sumStatus["Down", ] | 525 downCount[i] <- sumStatus["Down", ] |
| 526 flatCount[i] <- sumStatus["NotSig", ] | 526 flatCount[i] <- sumStatus["NotSig", ] |
| 527 | 527 |
| 528 # Write top expressions table | 528 # Write top expressions table |
| 529 top <- topTags(res, n=Inf, sort.by="PValue") | 529 top <- topTags(res, adjust.method=opt$pAdjOpt, n=Inf, sort.by="PValue") |
| 530 write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE) | 530 write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE) |
| 531 | 531 |
| 532 linkName <- paste0("edgeR_", contrastData[i], ".tsv") | 532 linkName <- paste0("edgeR_", contrastData[i], ".tsv") |
| 533 linkAddr <- paste0("edgeR_", contrastData[i], ".tsv") | 533 linkAddr <- paste0("edgeR_", contrastData[i], ".tsv") |
| 534 linkData <- rbind(linkData, c(linkName, linkAddr)) | 534 linkData <- rbind(linkData, c(linkName, linkAddr)) |