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comparison edger.R @ 1:2a16413ec60d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 22882a8eabae0dcc15938423852d1325303b0b78
author iuc
date Tue, 30 Jan 2018 04:07:08 -0500
parents 9bdff28ae1b1
children a1634a9c2ee1
comparison
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0:9bdff28ae1b1 1:2a16413ec60d
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["1", ] 489 upCount[i] <- sumStatus["Up"]
490 downCount[i] <- sumStatus["-1", ] 490 downCount[i] <- sumStatus["Down"]
491 flatCount[i] <- sumStatus["0", ] 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