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comparison edger.R @ 6:555659de7321 draft

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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
comparison
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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))