R/AffymetrixCnChpSet.extras.R

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

setMethodS3("exportTotalCnRatioSet", "AffymetrixCnChpSet", function(this, ..., overwrite=FALSE, rootPath="rawCnData", verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }


  verbose && enter(verbose, "Exporting log2(theta/thetaR) data from ", class(this)[1])
  dataSet <- getFullName(this)
  verbose && cat(verbose, "Data set: ", dataSet)
  nbrOfFiles <- length(this)
  verbose && cat(verbose, "Number of files: ", nbrOfFiles)
  cdf <- getCdf(this)
  nbrOfUnits <- nbrOfUnits(cdf)
  verbose && cat(verbose, "Number of units: ", nbrOfUnits)

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Identify Affymetrix CDF file
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Affymetrix CDF
  platform <- getPlatform(cdf)
  chipType <- getChipType(cdf)

  verbose && cat(verbose, "Platform: ", platform)
  verbose && cat(verbose, "Chip type: ", chipType)
  # Not needed anymore
  cdf <- NULL


  # Setup output directory
  chipTypeS <- getChipType(cdf, fullname=FALSE)
  outPath <- file.path(rootPath, dataSet, chipTypeS)
  outPath <- Arguments$getWritablePath(outPath)
  verbose && cat(verbose, "Output path: ", outPath)

  for (kk in seq_along(this)) {
    ce <- this[[kk]]
    verbose && enter(verbose, sprintf("File %d ('%s') of %d", kk, getName(ce), nbrOfFiles))

#    # Sanity check
#    stopifnot(nbrOfUnits(ce) == nbrOfUnits)

    filename <- sprintf("%s,log2ratio,total.asb", getFullName(ce))
    pathname <- file.path(outPath, filename)
    verbose && cat(verbose, "Pathname: ", pathname)

    if (!overwrite && isFile(pathname)) {
      verbose && cat(verbose, "Nothing to do. File already exists.")
      verbose && exit(verbose)
      next
    }

    verbose && enter(verbose, "Reading data from CN5.CHP file")
    data <- extractLogRatios(ce, verbose=verbose)
    verbose && str(verbose, data)
    # Sanity check
    stopifnot(length(data) == nbrOfUnits)
    verbose && exit(verbose)

    verbose && enter(verbose, "Allocating (temporary) output file")
    # (allow rename of existing one if forced)
    isFile <- (overwrite && isFile(pathname))
    pathnameT <- pushTemporaryFile(pathname, isFile=isFile, verbose=less(verbose,10))

    asb <- AromaUnitSignalBinaryFile$allocate(pathnameT, nbrOfRows=nbrOfUnits, platform=platform, chipType=chipType)

    verbose && print(verbose, asb)
    verbose && exit(verbose)


    verbose && enter(verbose, "Updating temporary output file")
    # Store data
    asb[,1] <- data

    footer <- readFooter(asb)
    footer$srcFile <- list(
      srcDataSet=dataSet,
      srcFullName=getFullName(ce),
      srcFilename=getFilename(ce),
      srcChecksum=getChecksum(ce)
    )
    writeFooter(asb, footer)
    verbose && exit(verbose)

    # Not needed anymore
    asb <- data <- footer <- NULL

    # Rename temporary file
    popTemporaryFile(pathnameT, verbose=verbose)

    verbose && exit(verbose)
  } # for (kk ...)

  verbose && enter(verbose, "Setting up output data sets")
  res <- list(
    total = AromaUnitTotalCnBinarySet$byPath(outPath),
    fracB = NA
  )
  verbose && exit(verbose)

  verbose && exit(verbose)

  invisible(res)
}) # exportTotalCnRatioSet()