R/AromaUflFile.AFFX.R

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

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# BEGIN: AFFX
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setMethodS3("allocateFromCdf", "AromaUflFile", function(static, cdf, nbrOfEnzymes=1L, ...) {
  # Argument 'cdf':
  cdf <- Arguments$getInstanceOf(cdf, "AffymetrixCdfFile")

  # Argument 'nbrOfEnzymes':
  nbrOfEnzymes <- Arguments$getInteger(nbrOfEnzymes, range=c(1,10))

  types <- rep("integer", times=nbrOfEnzymes)
  sizes <- rep(2L, times=nbrOfEnzymes)

  NextMethod("allocateFromCdf", types=types, sizes=sizes)
}, static=TRUE)



setMethodS3("importFromAffymetrixNetAffxCsvFile", "AromaUflFile", function(this, csv, enzymes=1:nbrOfEnzymes(this), enzymesToUpdate=1:nbrOfEnzymes(this), rows=NULL, ..., verbose=FALSE) {
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  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'csv':
  csv <- Arguments$getInstanceOf(csv, "AffymetrixNetAffxCsvFile")

  # Argument 'enzymesToUpdate':
  enzymesToUpdate <- Arguments$getIndices(enzymesToUpdate, max=nbrOfEnzymes(this))

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



  verbose && enter(verbose, "Importing (unit name, fragment length+) data from ", class(csv)[1])

  # Query CDF
  cdf <- getCdf(this)

  # Read unit names
  unitNames <- getUnitNames(csv, rows=rows, ..., verbose=less(verbose))
  verbose && cat(verbose, "Unit names:")
  verbose && str(verbose, unitNames)
  
  # 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]
  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?")
  }

#  verbose && summary(verbose, data)

  # Read data
  data <- readDataUnitFragmentLength(csv, enzymes=enzymes, rows=keep, ..., verbose=less(verbose))
  verbose && str(verbose, data)
#  verbose && summary(verbose, data)

  data <- data[,-1,drop=FALSE]
  verbose && str(verbose, data)

  # Garbage collect
  gc <- gc()
  verbose && print(verbose, gc, level=-10)

  # Update
  this[units,enzymesToUpdate] <- data
  # Not needed anymore
  data <- NULL

  gc <- gc()
  verbose && print(verbose, gc, level=-10)

  verbose && exit(verbose)

  invisible(units)
})

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# END: AFFX
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