Nothing
library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
csR <- AffymetrixCelSet$byName("GSE8605", chipType="Mapping10K_Xba142")
print(csR)
cesN <- doASCRMAv2(csR, arrays=1:6, drop=FALSE, verbose=verbose)$cesN
print(cesN)
ceR <- getAverage(cesN, verbose=verbose)
ce <- cesN[[1]]
ugp <- getAromaUgpFile(csR)
print(ugp)
for (chr in getChromosomes(ugp)) {
units <- getUnitsOnChromosome(ugp, chr)
pos <- getPositions(ugp, units=units) / 1e6
thetaR <- extractTotalAndFreqB(ceR, units=units)[,"total"]
data <- extractTotalAndFreqB(ce, units=units)
data[,"total"] <- 2*data[,"total"] / thetaR
chrTag <- sprintf("Chr%02d", chr)
toPNG(getFullName(cesN), tags=c(getFullName(ce), chrTag, "TCN"), aspectRatio=1, {
layout(matrix(1:2, ncol=1))
par(mar=c(3,4,2,1)+0.1, pch=".")
# TCN tracks
cn <- RawCopyNumbers(data[,"total"], pos, chromosome=chr)
plot(cn, col="gray", cex=0.8, ylim=c(0,4))
cnS <- gaussianSmoothing(cn, xOut=seq(xMin(cn), xMax(cn), by=1/2), sd=1)
points(cnS, col="black")
stext(side=3, pos=0, getName(ce))
stext(side=3, pos=1, chrTag)
# BAF tracks
plot(pos, data[,"freqB"], cex=3, ylim=c(0,1))
box(col="blue")
stext(side=3, pos=0, getTags(cesN, collapse=","))
})
} # for (chr ...)
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