comparison rgedgeRpaired_nocamera.xml @ 81:f86cb6b724ee draft

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80:335abf087bc5

         </param>
         <when value="T">
          <param name="edgeR_priordf" type="integer" value="10" size="3" 
           label="prior.df for tagwise dispersion - larger value = more squeezing of tag dispersions to common dispersion. Replaces prior.n  and prior.df = prior.n * residual.df"
           help="10 = edgeR default. Use a larger value to 'smooth' small samples. See edgeR docs and note below"/>
          <param name="edgeR_robust" type="select" value="20" size="3" 
           label="Use robust dispersion method"
           help="Use ordinary, anscombe or deviance robust deviance estimates">
             <option value="ordinary" selected="true">Use ordinary deviance estimates</option>
             <option value="deviance">Use robust deviance estimates</option>
             <option value="anscombe">use Anscombe robust deviance estimates</option>

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",robustmeth='ordinary') 
{
  # Error handling
  if (length(unique(group))!=2){
    print("Number of conditions identified in experiment does not equal 2")
    q()

#end if

#if $edgeR.doedgeR == "T":
  out_edgeR = "$out_edgeR"
  edgeR_priordf = $edgeR.edgeR_priordf  
  edgeR_robust_meth = "$edgeR.edgeR_robust"
#end if


if (sum(c(doedgeR,doVoom,doDESeq2)) == 0)
{

colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_")                   #Relable columns
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,robustmeth=edgeR_robust_meth)
sessionInfo()
]]>
</configfile>
</configfiles>
<help>

81:f86cb6b724ee

         </param>
         <when value="T">
          <param name="edgeR_priordf" type="integer" value="10" size="3" 
           label="prior.df for tagwise dispersion - larger value = more squeezing of tag dispersions to common dispersion. Replaces prior.n  and prior.df = prior.n * residual.df"
           help="10 = edgeR default. Use a larger value to 'smooth' small samples. See edgeR docs and note below"/>
          <param name="edgeR_robust_method" type="select" value="20" size="3" 
           label="Use robust dispersion method"
           help="Use ordinary, anscombe or deviance robust deviance estimates">
             <option value="ordinary" selected="true">Use ordinary deviance estimates</option>
             <option value="deviance">Use robust deviance estimates</option>
             <option value="anscombe">use Anscombe robust deviance estimates</option>

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",robust_meth='ordinary') 
{
  # Error handling
  if (length(unique(group))!=2){
    print("Number of conditions identified in experiment does not equal 2")
    q()

#end if

#if $edgeR.doedgeR == "T":
  out_edgeR = "$out_edgeR"
  edgeR_priordf = $edgeR.edgeR_priordf  
  edgeR_robust_meth = "$edgeR.edgeR_robust_method"
#end if


if (sum(c(doedgeR,doVoom,doDESeq2)) == 0)
{

colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_")                   #Relable columns
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>