R/AffymetrixCelSet.writeSgr.R

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

# @author "HB"
#
# \references{
#   [1] https://wiki.transvar.org/confluence/display/igbman/File+Formats
# }
setMethodS3("writeSgr", "AffymetrixCelSet", function(this, units=NULL, ..., tags=getTags(this), verbose=FALSE, fileExtension="sgr", fileSep="\t", nbrOfFigures=3) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  chrText <- paste(c(1:22, "X", "Y", "M"), sep="")
  names(chrText) <- 1:25

  nbrOfArrays <- length(this)
  cdf <- getCdf(this)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Read indices
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  verbose && enter(verbose, "Reading indices")
  indices <- getCellIndices(cdf, units=units, stratifyBy="pm")
  indices <- unlist(indices, use.names=FALSE)
  verbose && exit(verbose)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Read probe genomic location
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  verbose && enter(verbose, "Gathering probe genomic locations")
  acp <- AromaCellPositionFile$byChipType(getChipType(cdf))

  ch <- paste("chr", chrText[ as.character(acp[indices,1,drop=TRUE]) ], sep="")
  pos <- acp[indices,2,drop=TRUE]
  verbose && exit(verbose)

  for (ii in seq_len(nbrOfArrays)) {
    cf <- this[[ii]]
    sampleName <- getName(cf)

    verbose && enter(verbose, sprintf("Gathering and writing data for ", sampleName))

    fullname <- paste(c(sampleName, tags), collapse=",")
    filename <- sprintf("%s.%s", fullname, fileExtension)

    data <- extractMatrix(cf, cells=indices, verbose=verbose)
    data <- log2(data)
    data <- round(data, digits=nbrOfFigures)
    data <- cbind(ch, pos, data)
    write.table(data, filename, quote=FALSE, row.names=FALSE, col.names=FALSE, sep=fileSep)

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

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Store read units in cache
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
})