R/AromaCellMatchScoreFile.importFromBpmap.R

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

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

  # Argument 'rows':
  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 match scores from BPMAP file")

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

  verbose && enter(verbose, "Saving scores to ACM file")
  verbose && cat(verbose, "Pathname: ", getPathname(this))

  for(kk in seq_along(bps)) {
    bp <- bps[[kk]]
    verbose && enter(verbose, "Updating ", bp$seqInfo$fullname[1])

    ms <- round(bp$matchscore*1e6)
    # which() is faster than which()
    w <- which(ms >= 1 & ms <= 10)
    if(length(w) > 0) {
      cells <- bp$pmy[w]*rows + bp$pmx[w] + 1
      updateMatchScores(this, cells=cells, scores=ms[w])
    }
    # Not needed anymore
    ms <- w <- NULL

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

  invisible(this)
})