R/CnChipEffectFile.exportAromaSignalBinaryFileList.R

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

setMethodS3("exportAromaSignalBinaryFileList", "CnChipEffectFile", function(this, whats=c("total", "freqB"), ..., force=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'what':
  whats <- match.arg(whats, several.ok=TRUE)

  if ("freqB" %in% whats) {
    if (!force && this$combineAlleles) {
      whats <- setdiff(whats, "freqB")
      warnings("Ignoring value \"freqB\" in argument 'what', because source does not contain allele-specific chip effects. Use argument 'force=TRUE' to override this and generate a freqB file that contains all NAs: ", getPathname(this))
    }
  }

  NextMethod("exportAromaSignalBinaryFileList", whats=whats)
}, protected=TRUE)