Mercurial > repos > iuc > dexseq
diff dexseq.R @ 2:6e8b61c54ff3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
| author | iuc |
|---|---|
| date | Sun, 28 Jan 2018 04:04:39 -0500 |
| parents | 4ca0e679f21e |
| children | 278b189248cd |
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--- a/dexseq.R Sun Jan 29 06:59:35 2017 -0500 +++ b/dexseq.R Sun Jan 28 04:04:39 2018 -0500 @@ -3,9 +3,11 @@ # we need that to not crash galaxy with an UTF8 error on German LC settings. Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") -library("DEXSeq") -library('getopt') -library('rjson') +suppressPackageStartupMessages({ + library("DEXSeq") + library('getopt') + library('rjson') +}) options(stringAsfactors = FALSE, useFancyQuotes = FALSE) @@ -90,7 +92,7 @@ BPPARAM=MulticoreParam(workers=opt$threads) dxd <- estimateDispersions(dxd, formula=formulaFullModel, BPPARAM=BPPARAM) print("Estimated dispersions") -dxd <- testForDEU(dxd, fullModel=formulaFullModel, BPPARAM=BPPARAM) +dxd <- testForDEU(dxd, reducedModel=formulaReducedModel, fullModel=formulaFullModel, BPPARAM=BPPARAM) print("tested for DEU") dxd <- estimateExonFoldChanges(dxd, fitExpToVar=primaryFactor, BPPARAM=BPPARAM) print("Estimated fold changes") @@ -111,7 +113,7 @@ if ( !is.null(opt$reportdir) ) { save(dxd, resSorted, file = file.path(opt$reportdir,"DEXSeq_analysis.RData")) save.image() - DEXSeqHTML(res, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA")) + DEXSeqHTML(res, fitExpToVar=primaryFactor, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA")) unlink(file.path(opt$reportdir,"DEXSeq_analysis.RData")) } sessionInfo()