R/AromaUnitGcContentFile.AFFX.R

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

setMethodS3("allocateFromCdf", "AromaUnitGcContentFile", function(static, cdf, ...) {
  # Argument 'cdf':
  cdf <- Arguments$getInstanceOf(cdf, "AffymetrixCdfFile")

  types <- "double"
  sizes <- 4L

  res <- NextMethod("allocateFromCdf", types=types, sizes=sizes)
  res[,1] <- NA_real_

  res
}, static=TRUE)



setMethodS3("importFromAffymetrixNetAffxCsvFile", "AromaUnitGcContentFile", function(this, csv, rows=NULL, ..., verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'csv':
  csv <- Arguments$getInstanceOf(csv, "AffymetrixNetAffxCsvFile")

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


  verbose && enter(verbose, "Importing (unit name, GC content) data from ", class(csv)[1])

  # Query CDF
  cdf <- getCdf(this)

  # Read data
  data <- readDataFrame(csv, colClasses=c("^(probeSetID|%GC)$"="character"))
  unitNames <- data[,1]
  verbose && str(verbose, unitNames)
  values <- as.double(data[,2])
  verbose && str(verbose, values)
  # Not needed anymore
  data <- NULL
  
  # Keep the units in the CDF
  units <- indexOf(cdf, names=unitNames)
  verbose && cat(verbose, "Unit indices:")
  verbose && str(verbose, units)
  # Not needed anymore
  unitNames <- NULL

  keep <- which(!is.na(units))
  verbose && printf(verbose, "Keeping %d of %d (%.2f%%)\n", 
       length(keep), length(units), 100*length(keep)/length(units))
  units <- units[keep]
  # Not needed anymore
  keep <- NULL
  if (length(units) == 0) {
    warning("None of the unit names in the CSV match the ones in the CDF ('", getPathname(cdf), "'). Is the correct file ('", getPathname(csv), "'), being imported?")
  }

  # Update
  this[units,1] <- values
  # Not needed anymore
  values <- NULL

  verbose && exit(verbose)

  invisible(units)
})