R/HaarSegModel.R

In HenrikBengtsson/aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

###########################################################################/**
# @RdocClass HaarSegModel
#
# @title "The HaarSegModel class"
#
# \description{
#  @classhierarchy
#
#  This class represents the Haar wavelet-based segmentation (HaarSeg)
#  model [1].
# }
#
# @synopsis
#
# \arguments{
#   \item{cesTuple}{A @see "CopyNumberDataSetTuple".}
#   \item{breaksFdrQ}{Default tuning parameters specific to the HaarSeg
#         algorithm.}
#   \item{...}{Arguments passed to the constructor of
#              @see "CopyNumberSegmentationModel".}
# }
#
# \section{Fields and Methods}{
#  @allmethods "public"
# }
#
# @author
#
# \seealso{
#  @see "CopyNumberSegmentationModel".
# }
#
# \references{
#   [1] Ben-Yaacov E. and Eldar YC. \emph{A fast and flexible method for the segmentation of aCGH data}, Bioinformatics, 2008.
#   \url{https://webee.technion.ac.il/Sites/People/YoninaEldar/software_det1.php}
# }
#*/###########################################################################
setConstructorS3("HaarSegModel", function(cesTuple=NULL, ..., breaksFdrQ=0.0001) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Load required packages
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  if (!is.null(cesTuple)) {
    # Early error, iff package is not installed
    requireNamespace("HaarSeg") || throw("Package not loaded: HaarSeg")
  }

  # Argument 'breaksFdrQ':
  breaksFdrQ <- Arguments$getDouble(breaksFdrQ, range=c(0,1))

  extend(CopyNumberSegmentationModel(cesTuple=cesTuple, ...), "HaarSegModel",
    .breaksFdrQ = breaksFdrQ
  )
})


setMethodS3("getAsteriskTags", "HaarSegModel", function(this, ...) {
  NextMethod("getAsteriskTags", tag="HAAR")
}, protected=TRUE)


setMethodS3("getFitFunction", "HaarSegModel", function(this, ...) {
  segmentByHaarSeg
}, protected=TRUE)