diff dexseq.R @ 22:71cb8c5ae8bd draft

Uploaded

--- a/dexseq.R	Thu Sep 03 11:26:08 2015 -0400
+++ b/dexseq.R	Tue Sep 22 11:24:46 2015 -0400
@@ -85,22 +85,28 @@
 
 colData(dxd)
 dxd <- estimateSizeFactors(dxd)
+print("Estimated size factors")
 sizeFactors(dxd)
 BPPARAM=MulticoreParam(workers=opt$threads)
 dxd <- estimateDispersions(dxd, formula=formulaFullModel, BPPARAM=BPPARAM)
-dxd <- testForDEU(dxd, reducedModel=formulaReducedModel, fullModel=formulaFullModel, BPPARAM=BPPARAM)
+print("Estimated dispersions")
+dxd <- testForDEU(dxd, fullModel=formulaFullModel, BPPARAM=BPPARAM)
+print("tested for DEU")
 dxd <- estimateExonFoldChanges(dxd, fitExpToVar=primaryFactor, BPPARAM=BPPARAM)
+print("Estimated fold changes")
 res <- DEXSeqResults(dxd)
+print("Results")
 table(res$padj <= opt$fdr)
 resSorted <- res[order(res$padj),]
 head(resSorted)
 
 write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE)
+print("Written Results")
 
 if ( !is.null(opt$reportdir) ) {
     save(dxd, resSorted, file = file.path(opt$reportdir,"DEXSeq_analysis.RData"))
     save.image()
-    DEXSeqHTML(res, path=opt$reportdir, FDR=opt$fdr, color=c("#C3EEE7","#B7FEA0","#F1E7A1","#CEAEFF","#FF8F43","#EDC3C5","#AAA8AA","#FF0000","#637EE9","#FBFBFB"))
+    DEXSeqHTML(res, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA"))
     unlink(file.path(opt$reportdir,"DEXSeq_analysis.RData"))
 }
 sessionInfo()