Mercurial > repos > yhoogstrate > edger_with_design_matrix
changeset 7:61e42740b13a draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Thu, 09 Jan 2014 04:38:21 -0500 |
| parents | 149a52c74f39 |
| children | 8c71e4c3c054 |
| files | edgeR_DGE.xml |
| diffstat | 1 files changed, 4 insertions(+), 6 deletions(-) [+] |
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--- a/edgeR_DGE.xml Thu Jan 09 04:30:24 2014 -0500 +++ b/edgeR_DGE.xml Thu Jan 09 04:38:21 2014 -0500 @@ -64,8 +64,6 @@ output_8 = args[11] - - library(edgeR) raw_data <- read.delim(designmatrix,header=T,stringsAsFactors=T) @@ -149,10 +147,10 @@ lrt <- glmLRT(fit, contrast=cont[,1]) print(paste("Exporting to file: ",output_1,sep="")) -write.table(file=output_1,topTags(lrt,n=nrow(read_counts))$table,sep="\t",row.names=T) +write.table(file=output_1,topTags(lrt,n=nrow(read_counts))\$table,sep="\t",row.names=T) write.table(file=output_2,cpm(dge,normalized.lib.sizes=TRUE),sep="\t") ## todo EXPORT FPKM -write.table(file=output_4,dge$counts,sep="\t") +write.table(file=output_4,dge\$counts,sep="\t") @@ -160,8 +158,8 @@ print("Creating MA plots...") - etable <- topTags(lrt, n=nrow(dge))$table - etable <- etable[order(etable$FDR), ] + etable <- topTags(lrt, n=nrow(dge))\$table + etable <- etable[order(etable\$FDR), ] pdf(output_7) with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance")) with(subset(etable, FDR<0.05), points(logCPM, logFC, pch=20, col="red"))