diff dexseq.R @ 19:b7235a9b1881 draft

Uploaded

--- a/dexseq.R	Tue Sep 01 11:08:29 2015 -0400
+++ b/dexseq.R	Thu Sep 03 05:25:49 2015 -0400
@@ -19,20 +19,12 @@
     'gtf', 'a', 1, "character",
     'outfile', 'o', 1, "character",
     'reportdir', 'r', 1, "character",
-    'htmlfile', 'x', 1, "character",
     'factors', 'f', 1, "character",
     'threads', 'p', 1, "integer",
     'fdr', 'c', 1, "double"
 ), byrow=TRUE, ncol=4);
 opt = getopt(spec);
 
-
-#reportdir <- gsub(".dat", "_files", opt$outfile)
-
-dir.create(file.path(opt$reportdir))
-setwd(opt$reportdir)
-getwd()
-
 # if help was asked for print a friendly message
 # and exit with a non-zero error code
 if ( !is.null(opt$help) ) {
@@ -86,7 +78,6 @@
 primaryFactor
 countFiles
 opt$reportdir
-opt$htmlfile
 opt$threads
 getwd()
 
@@ -112,6 +103,4 @@
     DEXSeqHTML(res, path=opt$reportdir, FDR=opt$fdr, color=c("#C3EEE7","#B7FEA0","#F1E7A1","#CEAEFF","#FF8F43","#EDC3C5","#AAA8AA","#FF0000","#637EE9","#FBFBFB"))
     unlink(file.path(opt$reportdir,"DEXSeq_analysis.RData"))
 }
-file.remove(opt$htmlfile)
-file.symlink(file.path(opt$reportdir,"testForDEU.html"), opt$htmlfile)
 sessionInfo()