Mercurial > repos > fubar > differential_count_models

diff rgedgeR/rgedgeRpaired.xml @ 12:aa528c834664 draft

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Uploaded
author fubar
date Sat, 27 Jul 2013 01:56:58 -0400
parents e7733b353702
children f542654faa3b
line wrap: on
line diff
--- a/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 01:43:13 2013 -0400
+++ b/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 01:56:58 2013 -0400
@@ -375,7 +375,7 @@
 
 
 
-edgeIt = function (Count_Matrix,group,out_edgeR=F,out_VOOM=F,out_DESeq2=F,fdrtype='fdr',priordf=5, 
+edgeIt = function (Count_Matrix=c(),group=c(),out_edgeR=F,out_VOOM=F,out_DESeq2=F,fdrtype='fdr',priordf=5, 
         fdrthresh=0.05,outputdir='.', myTitle='Differential Counts',libSize=c(),useNDF=F,
         filterquantile=0.2, subjects=c(),mydesign=NULL,
         doDESeq2=T,doVoom=T,doCamera=T,doedgeR=T,org='hg19',
@@ -678,15 +678,15 @@
 doedgeR = $edgeR.doedgeR
 edgeR_priordf = 0
 
-#if $DESeq2.doDESeq2 == "T"
+#if $DESeq2.doDESeq2 == "T":
   out_DESeq2 = "$out_DESeq2"
   DESeq_fitType = "$DESeq2.DESeq_fitType"
 #end if
-#if $edgeR.doedgeR == "T"
+#if $edgeR.doedgeR == "T":
   out_edgeR = "$out_edgeR"
   edgeR_priordf = $edgeR.edgeR_priordf
 #end if
-#if $doVoom == "T"
+#if $doVoom == "T":
   out_VOOM = "$out_VOOM"
 #end if