comparison rgedgeRpaired_nocamera.xml @ 121:d69a656284f5 draft

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120:ee3aa2b01623

    }
  } #### doDESeq2 or doVoom
  
}
#### Done

###sink(stdout(),append=T,type="message")
builtin_gmt = ""
history_gmt = ""
history_gmt_name = ""

org = "$input1.dbkey"
if (org == "") { org = "hg19"}
fdrtype = "$fdrtype"
fdrthresh = $fdrthresh
useNDF = $useNDF
fQ = $fQ # non-differential centile cutoff
myTitle = "$title"
sids = strsplit("$subjectids",',')
subjects = unlist(sids)
nsubj = length(subjects)
TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1

cat('; CCols=')
cat(CCols)
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
snames = colnames(Count_Matrix)
nsamples = length(snames)
if (nsubj >  0 & nsubj != nsamples) {
options("show.error.messages"=T)
mess = paste('Fatal error: Supplied subject id list',paste(subjects,collapse=','),

Count_Matrix = Count_Matrix[,useCols] ### reorder columns
rn = rownames(Count_Matrix)
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 = factor(group, levels=c(ControlName,TreatmentName))
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>

**What it does**

121:d69a656284f5

    }
  } #### doDESeq2 or doVoom
  
}
#### Done
]]>

###sink(stdout(),append=T,type="message")
builtin_gmt = ""
history_gmt = ""
history_gmt_name = ""

org = "$input1.dbkey"
if (org == "") { org = "hg19"}
fdrtype = "$fdrtype"
fdrthresh = $fdrthresh
useNDF = $useNDF
fQ = $fQ
myTitle = "$title"
sids = strsplit("$subjectids",',')
subjects = unlist(sids)
nsubj = length(subjects)
TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1

cat('; CCols=')
cat(CCols)
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') 
snames = colnames(Count_Matrix)
nsamples = length(snames)
if (nsubj >  0 & nsubj != nsamples) {
options("show.error.messages"=T)
mess = paste('Fatal error: Supplied subject id list',paste(subjects,collapse=','),

Count_Matrix = Count_Matrix[,useCols] ### reorder columns
rn = rownames(Count_Matrix)
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)) )             
group = factor(group, levels=c(ControlName,TreatmentName))
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>

**What it does**