R/mpreprocess.R

In USCbiostats/ENmixUSC: Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

mpreprocess <-function(rgSet,nCores=1,bgParaEst="oob",dyeCorr="RELIC", 
        qc=FALSE,qnorm=TRUE,qmethod="quantile1",
        foutlier=TRUE,rmcr=FALSE,impute=FALSE)
{
    if(!(is(rgSet, "RGChannelSet") | is(rgSet, "MethylSet")))
    stop("ERROR: rgSet is not an object of class 'RGChannelSet' or 'MethylSet'")
    # if(nCores>detectCores()){
    # nCores <- detectCores();
    # cat("Only ",nCores," cores are avialable in your computer,", 
    #    "argument nCores was reset to nCores=",nCores,"\n")
    # }
    if(qc){
      if(is(rgSet, "RGChannelSetExtended")){qc <- QCinfo(rgSet)}else{
          qc=NULL; 
          cat("rgSet is not an object of class 'RGChannelSetExtended';\n",
              "QC will not be performed")}
        }else{qc=NULL}
    mdat <- preprocessENmix(rgSet, bgParaEst=bgParaEst, QCinfo=qc, 
        dyeCorr=dyeCorr,nCores=nCores)
    if(qnorm){mdat=norm.quantile(mdat,method=qmethod)}
    beta=rcp(mdat,qcscore=qc)
    if(foutlier){beta <- rm.outlier(beta,qcscore=qc,impute=impute,rmcr=rmcr)}
    beta
}