R/AromaCellSequenceFile.importFromBpmap.R

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

# @author "MR"
 setMethodS3("importFromBpMap", "AromaCellSequenceFile", function(this, srcPathname, rows=NULL, ..., verbose=TRUE) {
  # Argument 'srcPathname':
  srcPathname <- Arguments$getReadablePathname(srcPathname)

  # Argument 'rows':
  # HB: Can't we infer this from the BPMAP file? ...or have an option
  # to look it up in matching CDF.
  if (is.null(rows)) {
    stop("Must provide the chip dimensions: 'rows' argument is NULL")
  }

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }


  verbose && enter(verbose, "Importing cell sequences from BPMAP file")

  verbose && enter(verbose, "Reading BPMAP file")
  verbose && cat(verbose, "Pathname: ", srcPathname)
  bps <- .readBpmap(srcPathname)
  verbose && exit(verbose)

  verbose && enter(verbose, "Saving to ACS file")
  verbose && cat(verbose, "Pathname: ", getPathname(this))
  for(kk in seq_along(bps)) {
    bp <- bps[[kk]]
    verbose && enter(verbose,"Updating ", bp$seqInfo$fullname[1])

    cells <- bp$pmy*rows + bp$pmx + 1
    seqs <- bp$probeseq
    updateSequences(this, cells=cells, seqs=seqs)

    verbose && exit(verbose)
  }
  verbose && exit(verbose)

  verbose && exit(verbose)
  invisible(this)
})