R/imputeMAR.R

In imputeLCMD: A Collection of Methods for Left-Censored Missing Data Imputation

#' @title imputation under MAR/MCAR hypothesis
#' 
#' @description 
#' This function performs missing values imputation under MAR/MCAR hypothesis. 
#' The imputation of MVs is performed for each protein containing MAR/MCAR missing values
#' 
#' @param dataSet.mvs expression matrix containing abundances with MVs 
#'                         (either peptides or proteins)
#' @param model.selector binary vector; "1" indicates MAR/MCAR proteins
#' @param method the method to be used for MAR/MCAR missing values.
#'   Possible values: MLE (default), SVD, KNN
#'
#' @return dataset containing only MNAR (assumed to be left-censored)
#' missing data
#'  
#' @export
#' 
impute.MAR = function(dataSet.mvs, model.selector, method = "MLE"){
  
  if (length(which(model.selector[[1]]==1)) == 0){
    dataSet.imputed = dataSet.mvs
  }
  else{
    # ___________________________________________________________________________________
    # select MCAR proteins 
    # -----------------------------------------------------------------------------------
    dataSet.MCAR = dataSet.mvs[which(model.selector[[1]]==1),]
    
    # ___________________________________________________________________________________
    # perform imputation using the specified method
    # -----------------------------------------------------------------------------------
    
    switch(method,
           MLE = {
             dataSet.MCAR.imputed = impute.wrapper.MLE(dataSet.MCAR) 
           },
           
           SVD = {
             dataSet.MCAR.imputed = impute.wrapper.SVD(dataSet.MCAR, K = 2) 
           },
           
           KNN = {
             dataSet.MCAR.imputed = impute.wrapper.KNN(dataSet.MCAR, K = 15) 
           }     
    )
    
    # ___________________________________________________________________________________
    # replace imputed MCAR in the data matrix
    # -----------------------------------------------------------------------------------
    dataSet.imputed = dataSet.mvs
    dataSet.imputed[which(model.selector[[1]]==1),] = dataSet.MCAR.imputed
    
  }
  
  return(dataSet.imputed)
  
}