comparison edger.R @ 2:3de72f1f78aa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617

1:c469357cf454

    status = decideTestsDGE(res, adjust.method=opt$pAdjOpt, p.value=opt$pValReq,
                                             lfc=opt$lfcReq)
    sumStatus <- summary(status)

    # Collect counts for differential expression
    upCount[i] <- sumStatus["Up"]
    downCount[i] <- sumStatus["Down"]
    flatCount[i] <- sumStatus["NotSig"]
                                             
    # Write top expressions table
    top <- topTags(res, n=Inf, sort.by="PValue")
    write.table(top, file=topOut[i], row.names=FALSE, sep="\t")
    

2:3de72f1f78aa

    status = decideTestsDGE(res, adjust.method=opt$pAdjOpt, p.value=opt$pValReq,
                                             lfc=opt$lfcReq)
    sumStatus <- summary(status)

    # Collect counts for differential expression
    upCount[i] <- sumStatus["Up", ]
    downCount[i] <- sumStatus["Down", ]
    flatCount[i] <- sumStatus["NotSig", ]
                                             
    # Write top expressions table
    top <- topTags(res, n=Inf, sort.by="PValue")
    write.table(top, file=topOut[i], row.names=FALSE, sep="\t")