R/ASCRMAv2.R

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

# @author "HB"
setConstructorS3("ASCRMAv2", function(...) {
  extend(AromaPipeline(..., .class="AffymetrixCelSet"), "ASCRMAv2")
})


setMethodS3("assertAnnotationData", "ASCRMAv2", function(this, ...) {
  ds <- getInputDataSet(this)

  # Assert that the CDF file exists
  cdf <- getCdf(ds)

  # Assert that an UGP annotation data file exists
  gi <- getGenomeInformation(cdf)

  # Assert that an UFL annotation data file exists
  si <- getSnpInformation(cdf)

  # Assert than an ACS (probe-sequence) annotation files
  acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
})


setMethodS3("getSteps", "ASCRMAv2", function(this, ...) {
  list(
    "acc" = function(csR) {
      # Allelic cross-talk calibration tests
      acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
      print(acc)
      csC <- process(acc, verbose=log)
      print(csC)
      csC
    },

    "bpn" = function(csC) {
      # Base-position normalization
      bpn <- BasePositionNormalization(csC, target="zero")
      print(bpn)
      csN <- process(bpn, verbose=log)
      print(csN)
      csN
    },

    "avg" = function(csN) {
      # Allele-specific probe summarization
      plm <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=FALSE)
      print(plm)
      if (length(findUnitsTodo(plm)) > 0) {
        # Fit CN probes quickly (~5-10s/array + some overhead)
        units <- fitCnProbes(plm, verbose=log)
        str(units)
        units <- fit(plm, verbose=log)
        str(units)
      }
      ces <- getChipEffectSet(plm)
      print(ces)
      ces
    },

    "fln" = function(ces) {
      # Fragment-length normalization test
      fln <- FragmentLengthNormalization(ces, target="zero")
      print(fln)
      cesN <- process(fln, verbose=log)
      print(cesN)
      cesN
    }
  )
})