R/tailImpute.R

In SydneyBioX/phosphoR: A set of methods and tools for comprehensive analysis of phosphoproteomics data

#' Tail impute
#' 
#' Tail imputation approach as implemented in Perseus.
#' 
#' @usage tailImpute(mat)
#' 
#' @param mat a matrix with rows correspond to phosphosites and columns correspond to samples.
#' @param m a numeric number of for controlling mean downshifting.
#' @param s a numeric number of for controlling standard deviation of downshifted sampling values.
#' @export
#' 
tailImpute <- function(mat, m=1.6, s=0.6) {
  
  ms <- colMeans(mat, na.rm=TRUE)
  sds <- apply(mat, 2, sd, na.rm=TRUE)
  mat.impute <- mat
  for (i in 1:ncol(mat.impute)) {
    r <- rnorm(n=sum(is.na(mat.impute[,i])), mean=(ms[i]-sds[i]*m), sd=(sds[i]*s))
    mat.impute[which(is.na(mat.impute[,i])),i] <- r
  }
  return(mat.impute)
}