inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,CE.R

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

library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-4, timestamp=TRUE)

dataSet <- "GSE8605"
chipType <- "Mapping10K_Xba142"
dsNList <- doASCRMAv2(dataSet, chipType=chipType, verbose=verbose)
print(dsNList)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# CBS
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dsT <- dsNList$total
seg <- CbsModel(dsT)
print(seg)

# Try to segment
fit(seg, arrays=c(1,2), chromosomes=19, verbose=verbose)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# ChromsomeExplorer
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ce <- ChromosomeExplorer(seg, zooms=2^(0:5))
print(ce)
process(ce, arrays=1:2, chromosomes=c(1:2,19,23), verbose=verbose)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# CBS with a common reference
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Use the robust average of the first five arrays as a reference
dsR <- dsT[1:5]
dfR <- getAverageFile(dsR)
print(dfR)

seg <- CbsModel(dsT, refTuple=dfR, tags=c(getTags(dsT), "commonRef"))
print(seg)

# Try to segment
fit(seg, arrays=c(1,2), chromosomes=19, verbose=verbose)

# Write to file
pathname <- writeRegions(seg, arrays=1, oneFile=FALSE, verbose=verbose)
print(pathname)