R/stImpute.R

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

#' Single treatment (st) impute
#'
#' Impute the missing values for a phosphosite across replicates within a single treatment (or control)
#' if there are n or more quantified values of that phosphosite in that treatment.
#'
#' @usage stImpute(mat, n)
#'
#' @param mat a matrix with rows correspond to phosphosites and columns correspond to replicates within a treatment.
#' @param n an integer indicating n or more quantified values required for imputing missing values of a given phosphosite.
#' @export
#'
stImpute <- function(mat, n) {
  for(i in 1:nrow(mat)) {
    idx <- which(!is.na(mat[i,]))
    if(length(idx) >= n) {
      ms <- mean(mat[i,], na.rm = TRUE)
      sds <- sd(mat[i,], na.rm=TRUE)
      nid <- which(is.na(mat[i,]))
      mat[i,nid] <- rnorm(length(nid), mean=ms, sd=sds)
    }
  }
  return(mat)
}