inst/testScripts/system/chipTypes/CytoScanHD_Array/21.doASCRMAv2,PSCN.R

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-50, timestamp=TRUE)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setting up data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataSetName <- "Affymetrix-CytoScanHD"
chipType <- "CytoScanHD_Array"

csR <- AffymetrixCelSet$byName(dataSetName, chipType=chipType)
print(csR)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Allele-specific CRMAv2
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dsNList <- doASCRMAv2(csR, verbose=verbose)
print(dsNList)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Average TCN signals
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dfR <- getAverageFile(dsNList$total)
thetaR <- extractMatrix(dfR, drop=TRUE)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Extract (TCN,BAF) for a single array
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
array <- 3
dfList <- lapply(dsNList, FUN=getFile, array)
sampleName <- getFullName(dfList$total)

data <- sapply(dfList, FUN=extractMatrix)
data[,"total"] <- 2 * data[,"total"] / thetaR
str(data)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Plot along genome
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ugp <- getAromaUgpFile(dsNList$total)

chr <- 8
chrTag <- sprintf("Chr%02d", chr)

units <- getUnitsOnChromosome(ugp, chr)
x <- ugp[units,2,drop=TRUE]
x <- x/1e6

dataT <- data[units,]
C <- dataT[,"total"]
B <- dataT[,"fracB"]

toPNG(sampleName, tags=c(chrTag, "TCN+BAF"), width=1024, aspectRatio=0.5, {
  par(mar=c(2.2,3,1.2,1))
  subplots(2, ncol=1)
  plot(x, C, pch=".", ylim=c(0,6))
  stext(side=3, pos=0, sampleName)
  stext(side=3, pos=1, chrTag)
  plot(x, B, pch=".", ylim=c(0,1))
})