Mercurial > repos > fubar > differential_count_models
changeset 13:f542654faa3b draft
Uploaded
author | fubar |
---|---|
date | Sat, 27 Jul 2013 02:18:41 -0400 |
parents | aa528c834664 |
children | 8272815ba8ce |
files | rgedgeR/rgedgeRpaired.xml |
diffstat | 1 files changed, 20 insertions(+), 17 deletions(-) [+] |
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--- a/rgedgeR/rgedgeRpaired.xml Sat Jul 27 01:56:58 2013 -0400 +++ b/rgedgeR/rgedgeRpaired.xml Sat Jul 27 02:18:41 2013 -0400 @@ -401,7 +401,7 @@ zN = allN - nzN print('# Quantiles for non-zero row counts:',quote=F) print(quantile(nzrs,probs=seq(0,1,0.1)),quote=F) - if (useNDF == "T") + if (useNDF == T) { gt1rpin3 = rowSums(Count_Matrix/expandAsMatrix(colTotmillionreads,dim(Count_Matrix)) >= 1) >= nscut lo = colSums(Count_Matrix[!gt1rpin3,]) @@ -512,7 +512,7 @@ print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=','))) nzd = data.frame(log(nonzerod + 1e-2,10)) boxPlot(rawrs=nzd,cleanrs=log(normData,10),maint='TMM Normalisation',myTitle=myTitle,pdfname="edgeR_raw_norm_counts_box.pdf") - write.table(soutput,out_edgeR, quote=FALSE, sep="\t",row.names=F) + write.table(soutput,file=out_edgeR, quote=FALSE, sep="\t",row.names=F) tt = cbind( Name=as.character(rownames(DGEList\$counts)), DE\$table, @@ -567,7 +567,7 @@ qqPlot(descr=paste(myTitle,'DESeq2 qqplot'),pvector=rDESeq\$pvalue,outpdf='DESeq2_qqplot.pdf') cat("# DESeq top 50\n") print.noquote(srDESeq[1:50,]) - write.table(srDESeq,out_DESeq2, quote=FALSE, sep="\t",row.names=F) + write.table(srDESeq,file=out_DESeq2, quote=FALSE, sep="\t",row.names=F) topresults.DESeq = rDESeq[which(rDESeq\$padj < fdrthresh), ] DESeqcountsindex = which(allgenes %in% rownames(topresults.DESeq)) DESeqcounts = rep(0, length(allgenes)) @@ -623,14 +623,14 @@ rownames(rvoom) = rownames(workCM) rvoom = cbind(rvoom,NReads=cmrowsums,URL=contigurls) srvoom = rvoom[order(rvoom\$P.Value),] - write.table(srvoom,out_VOOM, quote=FALSE, sep="\t",row.names=F) + cat("# VOOM top 50\n") + print(srvoom[1:50,]) + write.table(srvoom,file=out_VOOM, quote=FALSE, sep="\t",row.names=F) # Use an FDR cutoff to find interesting samples for edgeR, DESeq and voom/limma topresults.voom = srvoom[which(rvoom\$adj.P.Val < fdrthresh), ] voomcountsindex = which(allgenes %in% topresults.voom\$ID) voomcounts = rep(0, length(allgenes)) voomcounts[voomcountsindex] = 1 - cat("# VOOM top 50\n") - print(srvoom[1:50,]) sink() } @@ -671,23 +671,26 @@ history_gmt="" out_edgeR = F out_DESeq2 = F -out_VOOM = F +out_VOOM = "${out_VOOM}" doDESeq2 = $DESeq2.doDESeq2 # make these T or F doVoom = $doVoom doCamera = F doedgeR = $edgeR.doedgeR edgeR_priordf = 0 -#if $DESeq2.doDESeq2 == "T": - out_DESeq2 = "$out_DESeq2" - DESeq_fitType = "$DESeq2.DESeq_fitType" + +#if ${doVoom} == "T": + out_VOOM = "${out_VOOM}" #end if -#if $edgeR.doedgeR == "T": - out_edgeR = "$out_edgeR" - edgeR_priordf = $edgeR.edgeR_priordf + +#if ${DESeq2.doDESeq2} == "T": + out_DESeq2 = "${out_DESeq2}" + DESeq_fitType = "${DESeq2.DESeq_fitType}" #end if -#if $doVoom == "T": - out_VOOM = "$out_VOOM" + +#if ${edgeR.doedgeR} == "T": + out_edgeR = "${out_edgeR}" + edgeR_priordf = ${edgeR.edgeR_priordf} #end if Out_Dir = "$html_file.files_path" @@ -700,7 +703,7 @@ if (org == "") { org = "hg19"} fdrtype = "$fdrtype" fdrthresh = $fdrthresh -useNDF = "$useNDF" +useNDF = $useNDF fQ = $fQ # non-differential centile cutoff myTitle = "$title" subjects = c($subjectids) @@ -740,7 +743,7 @@ group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) ) #Build a group descriptor group = factor(group, levels=c(ControlName,TreatmentName)) colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_") #Relable columns -results = edgeIt(Count_Matrix=Count_Matrix,group=group,out_edgeR=out_edgeR, out_VOOM=out_VOOM, out_DESeq2=out_DESeq2, +results = edgeIt(Count_Matrix=Count_Matrix,group=group, out_edgeR=out_edgeR, out_VOOM=out_VOOM, out_DESeq2=out_DESeq2, fdrtype='BH',priordf=edgeR_priordf,fdrthresh=0.05,outputdir='.', myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=c(), doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org,