R/AromaUnitFracBCnBinarySet.R

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

###########################################################################/**
# @RdocClass AromaUnitFracBCnBinarySet
#
# @title "The AromaUnitFracBCnBinarySet class"
#
# \description{
#  @classhierarchy
#
#  An AromaUnitFracBCnBinarySet object represents a set of 
#  @see "AromaUnitFracBCnBinaryFile"s with \emph{identical} chip types.
# }
# 
# @synopsis
#
# \arguments{
#   \item{...}{Arguments passed to @see "AromaUnitSignalBinarySet".}
# }
#
# \details{
#   The term "allele B fraction" is also know as "allele B frequency", which
#   was coined by Peiffer et al. (2006).  Note that the term "frequency" is
#   a bit misleading since it is not a frequency in neither the statistical
#   nor the population sense, but rather only proportion relative to the
#   total amount of allele A and allele B signals, which is calculated for
#   each sample independently.
# }
#
# \section{Fields and Methods}{
#  @allmethods "public"
# }
#
# \references{
#   [1] Peiffer et al., \emph{High-resolution genomic profiling of 
#       chromosomal aberrations using Infinium whole-genome genotyping},
#       Genome Res, 2006.\cr
# }
# 
# @author
#*/###########################################################################
setConstructorS3("AromaUnitFracBCnBinarySet", function(...) {
  extend(AromaUnitSignalBinarySet(...), "AromaUnitFracBCnBinarySet")
})


setMethodS3("byName", "AromaUnitFracBCnBinarySet", function(static, name, tags=NULL, ..., chipType=NULL, paths=c("totalAndFracBData", "rawCnData", "cnData", "smoothCnData"), pattern=".*,(frac|freq)B[.]asb$") {
  suppressWarnings({
    path <- findByName(static, name=name, tags=tags, chipType=chipType, 
                                           ..., paths=paths, mustExist=TRUE)
  })

  suppressWarnings({
    byPath(static, path=path, ..., pattern=pattern)
  })
}, static=TRUE) 


setMethodS3("writeDataFrame", "AromaUnitFracBCnBinarySet", function(this, filename=sprintf("%s,fracB.txt", getFullName(this)), ...) {
  NextMethod("writeDataFrame", filename=filename)
})