# HG changeset patch
# User fubar
# Date 1416744383 18000
# Node ID d69a656284f526e2bfe7fc556d881a3849eab11d
# Parent  ee3aa2b016236112f269d4b08c1f783fa060585e
Uploaded

diff -r ee3aa2b01623 -r d69a656284f5 rgedgeRpaired_nocamera.xml
--- a/rgedgeRpaired_nocamera.xml	Sun Nov 23 03:06:27 2014 -0500
+++ b/rgedgeRpaired_nocamera.xml	Sun Nov 23 07:06:23 2014 -0500
@@ -831,6 +831,7 @@
   
 }
 #### Done
+]]>
 
 ###sink(stdout(),append=T,type="message")
 builtin_gmt = ""
@@ -881,7 +882,7 @@
 fdrtype = "$fdrtype"
 fdrthresh = $fdrthresh
 useNDF = $useNDF
-fQ = $fQ # non-differential centile cutoff
+fQ = $fQ
 myTitle = "$title"
 sids = strsplit("$subjectids",',')
 subjects = unlist(sids)
@@ -895,7 +896,7 @@
 cat('\n')
 useCols = c(TCols,CCols)
 if (file.exists(Out_Dir) == F) dir.create(Out_Dir)
-Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t') #Load tab file assume header
+Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t') 
 snames = colnames(Count_Matrix)
 nsamples = length(snames)
 if (nsubj >  0 & nsubj != nsamples) {
@@ -911,16 +912,16 @@
 islib = rn %in% c('librarySize','NotInBedRegions')
 LibSizes = Count_Matrix[subset(rn,islib),][1] # take first
 Count_Matrix = Count_Matrix[subset(rn,! islib),]
-group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) )             #Build a group descriptor
+group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) )             
 group = factor(group, levels=c(ControlName,TreatmentName))
-colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_")                   #Relable columns
+colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_")                  
 results = edgeIt(Count_Matrix=Count_Matrix,group=group, out_edgeR=out_edgeR, out_Voom=out_Voom, out_DESeq2=out_DESeq2,
                  fdrtype='BH',mydesign=NULL,priordf=edgeR_priordf,fdrthresh=fdrthresh,outputdir='.',
                  myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=subjects,
                  doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org,
                  histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType,robust_meth=edgeR_robust_meth)
 sessionInfo()
-]]>
+
 </configfile>
 </configfiles>
 <help>