R/AffymetrixCelSetTuple.R

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

###########################################################################/**
# @RdocClass AffymetrixCelSetTuple
#
# @title "The AffymetrixCelSetTuple class"
#
# \description{
#  @classhierarchy
# }
#
# @synopsis
#
# \arguments{
#   \item{...}{Arguments passed to the constructor of
#      @see "aroma.core::AromaMicroarrayDataSetTuple".}
#   \item{.setClass}{The name of the class of the input set.}
# }
#
# \section{Fields and Methods}{
#  @allmethods "public"
# }
#
# @author "HB"
#
#*/###########################################################################
setConstructorS3("AffymetrixCelSetTuple", function(..., .setClass="AffymetrixCelSet") {
  extend(AromaMicroarrayDataSetTuple(..., .setClass=.setClass),
                                                     "AffymetrixCelSetTuple")
})




setMethodS3("byPath", "AffymetrixCelSetTuple", function(static, path, ..., verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'path':
  path <- Arguments$getReadablePath(path, mustExist=TRUE)

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

  # Get the corresponding CEL set class
  className <- class(static)[1]
  className <- gsub("Tuple$", "", className)
  clazz <- Class$forName(className)

  verbose && enter(verbose, "Creating ", class(static)[1])
  verbose && cat(verbose, "Path: ", path)

  # Get all subdirectories
  verbose && enter(verbose, "Scanning path for subdirectories")
  dirs <- list.files(path=path, full.names=TRUE)
  dirs <- dirs[sapply(dirs, FUN=isDirectory)]
  verbose && print(verbose, dirs)
  verbose && exit(verbose)

  # Check which corresponds to chip types, i.e. has CDF files
  verbose && enter(verbose, "Keeping those with names of chip types")
  dirs <- sapply(dirs, FUN=function(dir) {
    chipType <- basename(dir)
    pathname <- AffymetrixCdfFile$findByChipType(chipType)
    if (is.null(pathname))
      dir <- NA
    dir
  })
  dirs <- dirs[!is.na(dirs)]
  verbose && print(verbose, dirs)
  verbose && exit(verbose)

  # Define CEL sets for each directory
  verbose && enter(verbose, "Defining list of ", className, ":s")
  csList <- lapply(dirs, FUN=function(dir) {
    clazz$byPath(dir, ..., verbose=less(verbose))
  })
  names(csList) <- basename(names(csList))
  verbose && str(verbose, dirs)
  verbose && exit(verbose)

  verbose && exit(verbose)

  newInstance(static, csList, ...)
}, static=TRUE)



setMethodS3("getListOfCdfs", "AffymetrixCelSetTuple", function(this, ...) {
  csList <- getSets(this)
  lapply(csList, FUN=getCdf)
}, private=TRUE)


setMethodS3("getListOfUnitNamesFiles", "AffymetrixCelSetTuple", function(this, ...) {
  csList <- getSets(this)
  lapply(csList, FUN=getCdf)
}, private=TRUE)


setMethodS3("getListOfUnitTypesFiles", "AffymetrixCelSetTuple", function(this, ...) {
  csList <- getSets(this)
  lapply(csList, FUN=getCdf)
}, private=TRUE)