comparison rgedgeR/rgedgeRpaired.xml @ 12:aa528c834664 draft

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11:e7733b353702

  sink()
}



edgeIt = function (Count_Matrix,group,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',
        histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
        doCook=F,DESeq_fitType="parameteric") 

doVoom = $doVoom
doCamera = F 
doedgeR = $edgeR.doedgeR
edgeR_priordf = 0

#if $DESeq2.doDESeq2 == "T"
  out_DESeq2 = "$out_DESeq2"
  DESeq_fitType = "$DESeq2.DESeq_fitType"
#end if
#if $edgeR.doedgeR == "T"
  out_edgeR = "$out_edgeR"
  edgeR_priordf = $edgeR.edgeR_priordf
#end if
#if $doVoom == "T"
  out_VOOM = "$out_VOOM"
#end if

Out_Dir = "$html_file.files_path"
Input =  "$input1"

12:aa528c834664

  sink()
}



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',
        histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
        doCook=F,DESeq_fitType="parameteric") 

doVoom = $doVoom
doCamera = F 
doedgeR = $edgeR.doedgeR
edgeR_priordf = 0

#if $DESeq2.doDESeq2 == "T":
  out_DESeq2 = "$out_DESeq2"
  DESeq_fitType = "$DESeq2.DESeq_fitType"
#end if
#if $edgeR.doedgeR == "T":
  out_edgeR = "$out_edgeR"
  edgeR_priordf = $edgeR.edgeR_priordf
#end if
#if $doVoom == "T":
  out_VOOM = "$out_VOOM"
#end if

Out_Dir = "$html_file.files_path"
Input =  "$input1"