R/RawMirroredAlleleBFractions.R

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

###########################################################################/**
# @RdocClass RawMirroredAlleleBFractions
#
# @title "The RawMirroredAlleleBFractions class"
#
# \description{
#  @classhierarchy
# }
#
# @synopsis
#
# \arguments{
#   \item{...}{Arguments passed to @see "RawAlleleBFractions".}
# }
#
# \section{Fields and Methods}{
#  @allmethods "public"
# }
#
# @author
#*/###########################################################################
setConstructorS3("RawMirroredAlleleBFractions", function(...) {
  extend(RawAlleleBFractions(...), "RawMirroredAlleleBFractions")
})

setMethodS3("plot", "RawMirroredAlleleBFractions", function(x, ..., ylim=c(0,1/2)+c(-0.2,0.2), ylab="Mirrored Allele B fraction") {
  NextMethod("plot", ylim=ylim, ylab=ylab)
})

setMethodS3("extractRawMirroredAlleleBFractions", "default", abstract=TRUE)


setMethodS3("extractRawMirroredAlleleBFractions", "RawAlleleBFractions", function(this, ...) {
  beta <- getSignals(this)
  dh <- abs(beta - 1/2)
  res <- clone(this)
  res <- setSignals(res, dh)
  class(res) <- c("RawMirroredAlleleBFractions", class(res))
  res
})