Mercurial > repos > fubar > differential_count_models

comparison rgedgeRpaired_nocamera.xml @ 65:675cc60959f0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Mon, 10 Feb 2014 20:37:26 -0500
parents d4fc5eb21a2e
children 151bf55e018a
comparison
equal deleted inserted replaced
64:d4fc5eb21a2e 65:675cc60959f0
695 #DESeq2 = DESeq(deSEQds,fitType='local',pAdjustMethod=fdrtype) 695 #DESeq2 = DESeq(deSEQds,fitType='local',pAdjustMethod=fdrtype)
696 #rDESeq = results(DESeq2) 696 #rDESeq = results(DESeq2)
697 #newCountDataSet(workCM, group) 697 #newCountDataSet(workCM, group)
698 deSeqDatsizefac = estimateSizeFactors(deSEQds) 698 deSeqDatsizefac = estimateSizeFactors(deSEQds)
699 deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType) 699 deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType)
700 resDESeq = nbinomWaldTest(deSeqDatdisp, pAdjustMethod=fdrtype) 700 resDESeq = nbinomWaldTest(deSeqDatdisp)
701 rDESeq = as.data.frame(results(resDESeq)) 701 rDESeq = as.data.frame(results(resDESeq))
702 rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums,URL=contigurls) 702 rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums,URL=contigurls)
703 srDESeq = rDESeq[order(rDESeq\$pvalue),] 703 srDESeq = rDESeq[order(rDESeq\$pvalue),]
704 qqPlot(descr=paste(myTitle,'DESeq2 adj p qq plot'),pvector=rDESeq\$padj,outpdf='DESeq2_qqplot.pdf') 704 qqPlot(descr=paste(myTitle,'DESeq2 adj p qq plot'),pvector=rDESeq\$padj,outpdf='DESeq2_qqplot.pdf')
705 cat("# DESeq top 50\n") 705 cat("# DESeq top 50\n")