R/ProbeAffinityFile.R

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

###########################################################################/**
# @RdocClass ProbeAffinityFile
#
# @title "The ProbeAffinityFile class"
#
# \description{
#  @classhierarchy
#
#  This class represents estimates of probe affinities in probe-level models.
# }
#
# @synopsis
#
# \arguments{
#   \item{...}{Arguments passed to @see "ParameterCelFile".}
#   \item{probeModel}{The specific type of probe model.}
# }
#
# \section{Fields and Methods}{
#  @allmethods "public"
# }
#
# @author "HB"
#
# \seealso{
#   An object of this class is typically obtained through the
#   \code{getProbeAffinityFile()} method for the @see "ProbeLevelModel" class.
# }
#
#*/###########################################################################
setConstructorS3("ProbeAffinityFile", function(..., probeModel=c("pm", "mm", "pm-mm", "min1(pm-mm)", "pm+mm")) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'probeModel':
  probeModel <- match.arg(probeModel)

  extend(ParameterCelFile(...), "ProbeAffinityFile",
    "cached:.firstCells" = NULL,
    probeModel = probeModel
  )
})

setMethodS3("as.character", "ProbeAffinityFile", function(x, ...) {
  # To please R CMD check
  this <- x

  s <- NextMethod("as.character")
  s <- c(s, sprintf("Parameters: %s", getParametersAsString(this)))
  s
}, protected=TRUE)


setMethodS3("getParameters", "ProbeAffinityFile", function(this, ...) {
  params <- NextMethod("getParameters")
  params$.firstCells <- NULL
  params$probeModel <- this$probeModel
  params
}, protected=TRUE)



###########################################################################/**
# @RdocMethod getCellIndices
#
# @title "Retrieves tree list of cell indices for a set of units"
#
# \description{
#   @get "title" from the associated CDF.
# }
#
# @synopsis
#
# \arguments{
#  \item{...}{Additional arguments passed to \code{getCellIndices()}
#             of @see "AffymetrixCdfFile".}
#  \item{verbose}{See @see "R.utils::Verbose".}
# }
#
# \value{
#   Returns a @list structure, where each element corresponds to a unit.
#   If argument \code{unlist=TRUE} is passed, an @integer @vector is returned.
# }
#
# \seealso{
#   @seeclass
# }
#
# @keyword internal
#*/###########################################################################
setMethodS3("getCellIndices", "ProbeAffinityFile", function(this, ..., verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  verbose && enter(verbose, "Getting cell indices")
  verbose && cat(verbose, "Probe model: ", this$probeModel)

  stratifyBy <- switch(this$probeModel, "pm"="pm", "mm"="mm", "pm-mm"="pm", "min1(pm-mm)"="pm", "pm+mm"="pm")
  verbose && cat(verbose, "stratifyBy: ", stratifyBy)

  cdf <- getCdf(this)

  res <- getCellIndices(cdf, ..., stratifyBy=stratifyBy,
                                             verbose=less(verbose, 5))
  verbose && exit(verbose)

  res
}, protected=TRUE) # getCellIndices()



setMethodS3("readUnits", "ProbeAffinityFile", function(this, units=NULL, cdf=NULL, ...) {
  if (is.null(cdf)) {
    cdf <- getCellIndices(this, units=units)
  }

  # Note that the actually call to the decoding is done in readUnits()
  # of the superclass.
  NextMethod("readUnits", cdf=cdf, readStdvs=TRUE, readPixels=TRUE)
})


setMethodS3("updateUnits", "ProbeAffinityFile", function(this, units=NULL, cdf=NULL, data, ..., verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  verbose && enter(verbose, "Updating units of ", class(this)[1])
  verbose && cat(verbose, "Units:")
  verbose && str(verbose, units)

  if (is.null(cdf)) {
    cdf <- getCellIndices(this, units=units, verbose=less(verbose, 1))
  }

  # Note that the actually call to the encoding is done in updateUnits()
  # of the superclass.
  res <- NextMethod("updateUnits", cdf=cdf, data=data, verbose=less(verbose, 1))

  verbose && exit(verbose)

  res
}, private=TRUE)