Nothing
library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
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# Setup
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dataSet <- "GSE13372,testset"
chipType <- "GenomeWideSNP_6,Full"
csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)
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# AS-CRMAv2
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res <- doASCRMAv2(csR, drop=FALSE, verbose=verbose)
print(res)
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# Summarize theta = thetaA+thetaB
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cesN <- res$cesN
as <- AlleleSummation(cesN)
print(as)
cesT <- process(as, verbose=verbose)
print(cesT)
Y <- extractMatrix(cesT, verbose=verbose)
print(head(Y))
# Validation
dsNList <- res$dsNList
Y0 <- extractMatrix(dsNList$total, verbose=verbose)
print(head(Y0))
# Sanity check
stopifnot(all.equal(Y, Y0))
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# Segmentation
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cbs <- CbsModel(cesT)
print(cbs)
ce <- ChromosomeExplorer(cbs, zooms=2^(0:5))
process(ce, arrays=1:2, chromosomes=18:23, verbose=verbose)
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