R/SmoothRmaModel.R

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

###########################################################################/**
# @RdocClass SmoothRmaModel
#
# @title "The SmoothRmaModel class"
#
# \description{
#  @classhierarchy
#
#  This class represents the Chromosomal Smoothing Robust Multichip Analysis
#  method.
# }
#
# @synopsis
#
# \arguments{
#   \item{...}{Arguments passed to the constructor of
#              @see "SmoothMultiarrayModel".}
# }
#
# \section{Fields and Methods}{
#  @allmethods "public"
# }
#
# @author "HB"
#*/###########################################################################
setConstructorS3("SmoothRmaModel", function(...) {
  extend(SmoothMultiarrayModel(...), "SmoothRmaModel")
})


setMethodS3("getAsteriskTags", "SmoothRmaModel", function(this, collapse=NULL, ...) {
  tags <- NextMethod("getAsteriskTags", collapse=NULL)

  # Replace first tags
  tags[1] <- "SRMA"

  # Collapsed or split?
  if (!is.null(collapse)) {
    tags <- paste(tags, collapse=collapse)
  } else {
    tags <- unlist(strsplit(tags, split=","))
  }

  tags
}, protected=TRUE)

setMethodS3("getRootPath", "SmoothRmaModel", function(this, ...) {
  "plmData"
}, protected=TRUE)


setMethodS3("getFitUnitGroupFunction", "SmoothRmaModel", function(this, ...) {
  smoothWRMA
}, protected=TRUE)