library("aroma.affymetrix")
verbose <- Verbose(threshold=-8, timestamp=TRUE)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataSet <- "Affymetrix-HapMap,CEU,set1"
chipType <- "GenomeWideSNP_5"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full,r2")
print(cdf)
csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
# Split up into names and tags
setFullNamesTranslator(csR, function(names, ...) {
gsub("^(NA[0-9]+)_(.*)", "\\1,\\2", names)
})
# Drop duplicates
keep <- !duplicated(getNames(csR))
csR <- csR[keep]
# Keep only certain samples
sampleNames <- c("NA06985", "NA06991", "NA06993",
"NA07019", "NA07022", "NA07056")
csR <- csR[sampleNames]
print(csR)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# AS-CRMAv2
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
res <- doASCRMAv2(csR, drop=FALSE, verbose=verbose)
print(res)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Segmentation
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dsNList <- res$dsNList
seg <- CbsModel(dsNList$total)
print(seg)
ce <- ChromosomeExplorer(seg)
print(ce)
process(ce, arrays=1, chromosomes=c(19,23), verbose=verbose)
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