I had script like this, I have paired samples and using allelic specif copy
number analysis.
In this vignette
(http://aroma-project.org/vignettes/PairedPSCBS-lowlevel/), manually
allele-specific copy numbers were estimated. I am thinking whether
exportTotalCnRatioSet function does the same thing...
ds <- doCRMAv2(dataSet, cdf=cdf, plm="AvgCnPlm",
combineAlleles=combineAlleles, verbose=verbose)
if(combineAlleles == FALSE){
dsA <- ds
ds <- ds$total
}
# tumor-normal match.
# Extract the tumors
dsT <- ds[indexOf(ds, pattern="T")]
# Extract the normals
if(paired == TRUE){
dsN <- ds[indexOf(ds, pattern="N")]
# We will assume that the names matches
stopifnot(gsub("T", '',getNames(dsT)) == gsub("N",'',
getNames(dsN)))
}else{
dsN <- ds[indexOf(ds, pattern="N")]
dsN <- getAverageFile(dsN)
}
## Calculate TCNs
dsTN <- exportTotalCnRatioSet(dsT, ref=dsN)
Br,
C.Y
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