R/champ.impute.R

In JoshuaTian/ChAMP: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

if(getRversion() >= "3.1.0") utils::globalVariables(c("myLoad","impute.knn"))

champ.impute <- function(beta=myLoad$beta,
                         pd=myLoad$pd,
                         method="Combine",
                         k=5,
                         ProbeCutoff=0.2,
                         SampleCutoff=0.1)
{
  message("[===========================]")
  message("[<<< ChAMP.IMPUTE START >>>>]")
  message("-----------------------------")
  
  if(method=="Combine")
  {
    message("<method>:Combine. (Suitable for Large Data Set)")
    ## Eliminate probes and samples with too many NA values
    colNA <- apply(beta,2,function(x) length(which(is.na(x)))/length(x))
    colValid <- which(colNA < SampleCutoff)
    message("(1): ",ncol(beta)-length(colValid)," Samples contain ",SampleCutoff," or above NA will be removed.")
    
    tmp_beta <- beta[,colValid]
    
    rowNA <- apply(tmp_beta,1,function(x) length(which(is.na(x)))/length(x))
    rowValid <- which(rowNA < ProbeCutoff)
    message("(2): ",nrow(tmp_beta)-length(rowValid)," Probes contain ",ProbeCutoff," or above NA will be removed.")
    
    beta <- tmp_beta[rowValid,]
    if(!is.null(pd)) pd <- pd[colValid,]
    data.m <- impute.knn(beta, k=k)$data
    message("(3): The rest NA are imputed by KNN method which parameter k as ",k,".")
  } else if(method=="Delete")
  {
    message("<method>:Delete. (Suitable for Small Data Set)")
    colNA <- apply(beta,2,function(x) length(which(is.na(x)))/length(x))
    colValid <- which(colNA < SampleCutoff)
    message("(1): ",ncol(beta)-length(colValid)," Samples contain ",SampleCutoff," or above NA will be removed.")
    beta <- beta[,colValid]
    if(!is.null(pd)) pd <- pd[colValid,]
    data.m <- beta[-unique(which(is.na(beta),arr.ind=T)[,1]),]
    message("(2): ",nrow(beta)-nrow(data.m)," Probe are removed. Even they contain only one NA.")
  } else if(method=="KNN")
  {
    message("<method>:KNN. (Suitable for Large Data Set)")
    data.m <- impute.knn(beta,k=k)$data
    message("All NA are imputed by KNN method with parameter k as ",k,".")
  }
  message("[<<<<< ChAMP.IMPUTE END >>>>]")
  message("[===========================]")
  if(!is.null(pd)) return(list(beta=data.m,pd=pd)) else return(beta=data.m)
}