inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA.R

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

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



dataSet <- "HapMap,CEU,testset"
chipTypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")

# Expected sample names
sampleNames <- c("NA06985", "NA06991", "NA06993",
                 "NA06994", "NA07000", "NA07019")

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Tests for setting up CEL sets and locating the CDF file
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
csRList <- list()
for (chipType in chipTypes) {
  cs <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
  print(cs)
  stopifnot(identical(getNames(cs), sampleNames))
  csRList[[chipType]] <- cs
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Allelic cross-talk calibration tests
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
csList <- csRList
csCList <- list()
for (chipType in names(csList)) {
  cs <- csList[[chipType]]
  acc <- AllelicCrosstalkCalibration(cs)
  print(acc)
  csC <- process(acc, verbose=log)
  print(csC)
  stopifnot(identical(getNames(csC), getNames(cs)))
  csCList[[chipType]] <- csC
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Probe-level modelling test (for CN analysis)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
csList <- csCList
cesCnList <- list()
for (chipType in names(csList)) {
  cs <- csList[[chipType]]
  plm <- RmaCnPlm(cs, mergeStrands=TRUE, combineAlleles=TRUE, shift=300)
  print(plm)
  fit(plm, verbose=log)
  ces <- getChipEffectSet(plm)
  print(ces)
  stopifnot(identical(getNames(ces), getNames(cs)))
  cesCnList[[chipType]] <- ces
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Extraction test
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
thetaList <- list()
cesList <- cesCnList
for (chipType in names(cesList)) {
  ces <- cesList[[chipType]]
  theta <- extractMatrix(ces, verbose=log)
  print(summary(theta))
  thetaList[[chipType]] <- theta
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Fragment-length normalization test
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cesNList <- list()
for (chipType in names(csList)) {
  ces <- cesCnList[[chipType]]
  fln <- FragmentLengthNormalization(ces)
  print(fln)
  cesN <- process(fln, verbose=log)
  print(cesN)
  stopifnot(identical(getNames(cesN), getNames(ces)))
  cesNList[[chipType]] <- cesN
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Raw copy numbers
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Emulate list of ChipEffectSet:s where some arrays on exists in
# one of the sets
for (kk in seq_along(cesNList)) {
  ces <- cesNList[[kk]]
  ces <- ces[setdiff(seq_along(ces), length(ces)+1-kk)]
  cesNList[[kk]] <- ces
}


cnm <- RawCopyNumberModel(cesNList)
print(cnm)

rawCNs <- extractRawCopyNumbers(cnm, array=1, chromosome=1, verbose=log)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Glad model test
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#seg <- GladModel(cesNList)
seg <- CbsModel(cesNList)
print(seg)

fit(seg, arrays=1, chromosomes=19, verbose=log)

# Tests the case where one of the set does not have observations.
fit(seg, arrays=nbrOfArrays(seg), chromosomes=19, verbose=log)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# ChromosomeExplorer test
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ce <- ChromosomeExplorer(seg)
print(ce)
process(ce, arrays=1:2, chromosomes=c(19,23), verbose=log)