R/backgroundBiasCorrection.R

In benja0x40/MRA.TA: Multi Resolution Analysis of Tiling Arrays

# =============================================================================.
#' Background bias correction
# -----------------------------------------------------------------------------.
#' @author Benjamin Leblanc
#' @export backgroundBiasCorrection
#' @seealso
#'    \link{backgroundBiasEstimation},
#'    \link{normalizeArrayData}
# -----------------------------------------------------------------------------.
#' @description
#' Correct for a background bias in A, M values from a tiling array.
#' The correction consists in a rotation of angle \code{-theta}, as estimated
#' by the \link{backgroundBiasEstimation} function.
#'
#' @references
#' Leblanc B., Comet I., Bantignies F., and Cavalli G.,
#' Chromosome Conformation Capture on Chip (4C): data processing.
#' Book chapter in Polycomb Group Proteins: Methods and Protocols.
#' Lanzuolo C., Bodega B. editors, Methods in Molecular Biology (2016).
#' \link{http://dx.doi.org/10.1007/978-1-4939-6380-5_21}
# -----------------------------------------------------------------------------.
#' @param x
#' numeric vector of A values, e.g. the average of log2 of the specific and the
#' reference signals.
#'
#' @param y
#' numeric vector of M values, e.g. the log2 ratio of the specific over the
#' reference signal.
#'
#' @param theta
#' estimated bias angle in radians.
#'
#' @param AM.scale.compensation
#' \code{logical} determining if A and M values should be rescaled prior to
#' correction by a rotation of angle \code{-theta}.
#' Scale compensation is required and activated by default.
# -----------------------------------------------------------------------------.
#' @return
#' \code{backgroundBiasCorrection} returns a \code{list} with the following
#' elements:
#' \item{x}{ corrected A value}
#' \item{y}{ corrected M value}
# -----------------------------------------------------------------------------.
#' @examples
# -----------------------------------------------------------------------------.
backgroundBiasCorrection <- function(x, y, theta, AM.scale.compensation = T) {
  # Scale compensation (required for A and M values)
  if(AM.scale.compensation) {
    x <- x * sqrt(2)
    y <- y * sqrt(2)/2
  }
  v <- rotate(x, y, -theta)
  v
}