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comparison edger.R @ 2:a1634a9c2ee1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
author iuc
date Thu, 19 Apr 2018 17:26:38 -0400
parents 2a16413ec60d
children d79ed3ec25fe
comparison
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1:2a16413ec60d 2:a1634a9c2ee1
484 status = decideTestsDGE(res, adjust.method=opt$pAdjOpt, p.value=opt$pValReq, 484 status = decideTestsDGE(res, adjust.method=opt$pAdjOpt, p.value=opt$pValReq,
485 lfc=opt$lfcReq) 485 lfc=opt$lfcReq)
486 sumStatus <- summary(status) 486 sumStatus <- summary(status)
487 487
488 # Collect counts for differential expression 488 # Collect counts for differential expression
489 upCount[i] <- sumStatus["Up"] 489 upCount[i] <- sumStatus["Up", ]
490 downCount[i] <- sumStatus["Down"] 490 downCount[i] <- sumStatus["Down", ]
491 flatCount[i] <- sumStatus["NotSig"] 491 flatCount[i] <- sumStatus["NotSig", ]
492 492
493 # Write top expressions table 493 # Write top expressions table
494 top <- topTags(res, n=Inf, sort.by="PValue") 494 top <- topTags(res, n=Inf, sort.by="PValue")
495 write.table(top, file=topOut[i], row.names=FALSE, sep="\t") 495 write.table(top, file=topOut[i], row.names=FALSE, sep="\t")
496 496