R/GenomeInformation.AFFX.R

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

###########################################################################/**
# @set "class=GenomeInformation"
# @RdocMethod getChipType
#
# @title "Gets the chip type of this genome information set"
#
# \description{
#   @get "title".
# }
#
# @synopsis
#
# \arguments{
#  \item{...}{Not used.}
# }
#
# \value{
#   Returns a @character string.
# }
#
# \seealso{
#   @seeclass
# }
#*/###########################################################################
setMethodS3("getChipType", "GenomeInformation", function(this, ...) {
  # Infer chip type from the first parent directory that has the same name
  # as the chip type of an existing annotation unit names file.
  pathname <- getPathname(this)
  lastPath <- pathname
  while (TRUE) {
    path <- dirname(lastPath)
    if (path == lastPath)
      break
    chipType <- basename(path)

    # Try to find annotation data file for this chip type
    dummy <- AffymetrixCdfFile$findByChipType(chipType)
    if (!is.null(dummy))
      return(chipType)

    lastPath <- path
  }

  throw("Failed to infer the chip type from the pathname of the genome information file: ", pathname)
})


###########################################################################/**
# @RdocMethod getData
#
# @title "Gets all or a subset of the genome information data"
#
# \description{
#   @get "title".
# }
#
# @synopsis
#
# \arguments{
#  \item{units}{The units for which the data should be returned.}
#  \item{fields}{The fields to be returned.}
#  \item{orderBy}{The fields by which the returned data frame should be
#      ordered.}
#  \item{...}{Named arguments used to select a subset of the units to be
#      returned.  Either a value to be compared to or a @function returning
#      @TRUE or @FALSE.}
# }
#
# \value{
#   Returns a @data.frame, where the row names correspond to unit indices
#   as defined by the annotation unit names file.
# }
#
# \seealso{
#   @seemethod "getUnitIndices".
#   @seeclass
# }
#*/###########################################################################
setMethodS3("getData", "GenomeInformation", function(this, units=NULL, fields=c("chromosome", "physicalPosition"), orderBy=NULL, ..., force=FALSE, verbose=FALSE) {
  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)

  data <- this$.data
  if (is.null(data) || force) {
    verbose && enter(verbose, "Retrieving genome information from file")

    # Read the unit names from the corresponding annotation file
    verbose && enter(verbose, "Reading unit names from annotation file")
    chipType <- getChipType(this)
#    unf <- UnitNamesFile$byChipType(chipType)
    cdf <- AffymetrixCdfFile$byChipType(chipType)
    unf <- cdf
    targetUnitNames <- getUnitNames(unf)
    verbose && exit(verbose)

    # Now read the genome information data
    verbose && enter(verbose, "Reading genome information data")
    data <- readDataFrame(this, verbose=less(verbose))
    verbose && str(verbose, data)
    verbose && exit(verbose)

    verbose && enter(verbose, "Reordering units according to the unit names file")
    idxs <- match(targetUnitNames, data[,1])
    data <- data[idxs,,drop=FALSE]
#    data <- data[,-1]
    rownames(data) <- 1:nrow(data)
    verbose && exit(verbose)

    verbose && enter(verbose, "Optimizing default return order")
    # Default ordering
    args <- as.list(data[,fields,drop=FALSE])
    o <- do.call(order, args=args)
    data <- data[o,,drop=FALSE]
    # Not needed anymore
    o <- NULL
    verbose && str(verbose, data)
    verbose && exit(verbose)

    if ("chromosome" %in% fields) {
      verbose && enter(verbose, "Replacing 'X', 'Y' & 'M' with 23, 24 & 25")
      chr <- data[,"chromosome"]
      chr[chr == "X"] <- 23
      chr[chr == "Y"] <- 24
      chr[chr == "M"] <- 25;  # Mitochondrial
      suppressWarnings({
        chr <- as.integer(chr)
      })
      data[,"chromosome"] <- chr
      # Not needed anymore
      chr <- NULL
      verbose && str(verbose, data)
      verbose && exit(verbose)
    }

    # Store in cache
    this$.data <- data

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

    verbose && exit(verbose)
  }

  # Subset by unit?
  if (!is.null(units)) {
    # Map the unit indicies to the row names
    rr <- match(units, rownames(data))
    data <- data[rr,,drop=FALSE]
  }

  # Stratify by field values?
  args <- list(...)
  if (length(args) > 0) {
    for (key in names(args)) {
      # Get the values to be stratified upon.
      values <- data[,key,drop=FALSE]

      # Get the test (value or function)
      test <- args[[key]]
      test <- na.omit(test)
      if (is.function(test)) {
        keep <- test(values)
      } else {
        keep <- (values == test)
        keep <- (keep & !is.na(keep))
      }
      data <- data[keep,,drop=FALSE]
    }
    # Not needed anymore
    keep <- NULL
  }

  # Reorder?
  if (!is.null(orderBy)) {
    o <- do.call(order, args=as.list(data[,orderBy,drop=FALSE]))
    data <- data[o,,drop=FALSE]
    # Not needed anymore
    o <- NULL
  }

  # Extract a subset of fields?
  if (!is.null(fields))
    data <- data[,fields, drop=FALSE]

  data
})



###########################################################################/**
# @RdocMethod fromCdf
#
# @title "Static method to define a genome information set from a CDF"
#
# \description{
#   @get "title".
# }
#
# @synopsis
#
# \arguments{
#  \item{cdf}{An @see "AffymetrixCdfFile".}
#  \item{...}{Additional argument passed to @seemethod "byChipType".}
# }
#
# \value{
#   Returns a @see "GenomeInformation" object.
# }
#
# \seealso{
#   @seemethod "byChipType".
#   @seeclass
# }
#*/###########################################################################
setMethodS3("fromCdf", "GenomeInformation", function(static, cdf, ...) {
  byChipType(static, chipType=getChipType(cdf), nbrOfUnits=nbrOfUnits(cdf), ...)
}, static=TRUE, protected=TRUE)



setMethodS3("isCompatibleWithCdf", "GenomeInformation", function(this, cdf, ...) {
  # Argument 'cdf':
  cdf <- Arguments$getInstanceOf(cdf, "AffymetrixCdfFile")

  # By default, be naive and always return...
  TRUE
}, protected=TRUE)