R/ComBat.mc.R

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

ComBat.mc <-
function(dat,batch,nCores=1,...)
{
    # if(nCores>detectCores()){
    # nCores <- detectCores();
    # cat("Only ",detectCores()," Cores avialable, nCores was reset to ",
    # detectCores(),"\n")
    # }
    cat("Analysis is running, please wait...!","\n")

    rname <- rownames(dat)
    nparts1=min(ceiling(ncol(dat)/500), floor(nrow(dat)/40000))
    parts1 <- rep(1:nparts1,ceiling(nrow(dat)/nparts1))[1:nrow(dat)]
    nCores=min(10, nCores, ceiling(nrow(dat)/(nparts1*20000)))
    dat.o=NULL
    c1 <- makeCluster(nCores)
    registerDoParallel(c1)
    for(i in 1:nparts1){
    dat1=dat[which(parts1==i),]
    parts <- rep(1:nCores,ceiling(nrow(dat1)/nCores))[1:nrow(dat1)]
    parts=sample(parts)
    dat.o1 <- foreach (s = 1:nCores,.combine=rbind,.export=c("ComBat"))%dopar%{
    s=s;idx=which(parts==s)
    ComBat(dat=dat1[idx,], batch=batch,...)
    }
    dat.o=rbind(dat.o,dat.o1)
    }
    stopCluster(c1)
    dat.o[rname,]
}