R/compute_CV.R

In BenjaminPlanterose/UMtools: An R-package for analysing Illumina DNA Methylation arrays at the fluorescence intensity level

#' CVlogT
#' @export
#' @description Computes coefficient of variation of the log of the total intensity signal
#' @details It computes the following:
#' \deqn{R = \frac{M_{SD} + U_{SD} + \alpha}{U + M + \alpha}}
#' \deqn{CV_{logT}= \frac{1}{\frac{\log(U + M + \alpha)}{R} - R/2}}
#'
#' For more details, check the reference paper.
#' @references Revisiting Genetic artefacts on DNA methylation microarrays. Genome Research
#' @param M_SD Methylated standard deviation intensity matrix (CpGs as rows, samples as columns)
#' @param U_SD Unmethylated fluorescence standard deviation intensity matrix (CpGs as rows, samples as columns)
#' @param M Methylated fluorescence mean intensity matrix (CpGs as rows, samples as columns)
#' @param U Unmethylated fluorescence mean intensity matrix (CpGs as rows, samples as columns)
#' @return A matrix \code{CV} (CpGs as rows, samples as columns)
#' @examples
#' rgSet = read.metharray.exp(getwd(), extended = TRUE)
#' Grn = assay(rgSet, "Green")       # Green mean across beads
#' Red = assay(rgSet, "Red")         # Red mean across beads
#' M_U = GR_to_UM(Red, Grn, rgSet, "Mean")
#' GrnSD = assay(rgSet, "GreenSD")   # Green SD across beads
#' RedSD = assay(rgSet, "RedSD")     # Red SD across beads
#' M_U_sd = GR_to_UM(RedSD, GrnSD, rgSet, "SD")
#' compute_CV(M_U_sd$M, M_U_sd$U, M_U$M, M_U_sd$U)
compute_CV = function(M_SD, U_SD, M, U, alpha = 100)
{
  R = (M_SD + U_SD + alpha)/(U + M + alpha)
  1/(log(U + M + alpha)/R - R/2)
}