R/normalizeDifferencesToAverage.R

In HenrikBengtsson/aroma.light-BioC_release: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

###########################################################################/**
# @RdocGeneric normalizeDifferencesToAverage
# @alias normalizeDifferencesToAverage.list
#
# @title "Rescales channel vectors to get the same average"
#
# \description{
#  @get "title".
# }
#
# \usage{
# @usage normalizeDifferencesToAverage,list
# }
#
# \arguments{
#   \item{x}{A @numeric @list of length K.}
#   \item{baseline}{An @integer in [1,K] specifying which channel should be
#      the baseline.  The baseline channel will be almost unchanged.
#      If @NULL, the channels will be shifted towards median of them all.}
#   \item{FUN}{A @function for calculating the average of one channel.}
#   \item{...}{Additional arguments passed to the \code{avg} @function.}
# }
#
# \value{
#  Returns a normalized @list of length K.
# }
#
# @examples "../incl/normalizeDifferencesToAverage.Rex"
#
# @author "HB"
#*/###########################################################################
setMethodS3("normalizeDifferencesToAverage", "list", function(x, baseline=1, FUN=median, ...) {
  # Argument 'x':
  if (!is.list(x)) {
    throw("Argument 'x' is not a list: ", class(x)[1]);
  }

  # Number dimensions
  ndim <- length(x);

  # Argument 'baseline':
  if (!is.null(baseline)) {
    baseline <- as.integer(baseline);
    if (baseline < 1 && baseline > ndim) {
      throw(sprintf("Argument 'baseline' is out of range [1,%d]: %d",
                                                           ndim, baseline));
    }
  }


  # Calculate the overall average level for each dimension
  mus <- sapply(x, FUN=function(y) {
    y <- y[is.finite(y)];
    FUN(y);
  });

  # Estimate the overall target level
  if (is.null(baseline)) {
    targetMu <- mus[baseline];
  } else {
    targetMu <- median(mus, na.rm=TRUE);
  }

  # Calculate the required overall shifts per dimension
  deltas <- mus - targetMu;

  # Shift all dimensions so that all have the same overall average
  xN <- mapply(x, as.list(deltas), FUN=function(y, dy) {
    y <- y - dy;
    list(y);
  });

  # Return estimated parameters
  fit <- list(mus=mus, baseline=baseline, targetMu=targetMu, deltas=deltas);
  attr(xN, "fit") <- fit;

  xN;
})


############################################################################
# HISTORY:
# 2010-04-04
# o Made the code independent of R.utils::Arguments.
# 2009-09-30
# o Created from the source of an aroma.tcga vignette from May 2009.
############################################################################