R/design.mat.R

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

design.mat <-
function(mod, numCov){
    
	tmp <- which(colnames(mod) == 'Batch')
	tmp1 <- as.factor(mod[,tmp])
	cat("Found",nlevels(tmp1),'batches\n')
	design <- build.design(tmp1,start=1)
    
	if(!is.null(numCov)) {
		theNumCov = as.matrix(mod[,numCov])
		mod0 = as.matrix(mod[,-c(numCov,tmp)])
	} else 	mod0 = as.matrix(mod[,-tmp])
    
	ncov <- ncol(mod0)
    
	cat("Found",ncov,' categorical covariate(s)\n')
	if(!is.null(numCov)) cat("Found",ncol(theNumCov),' continuous covariate(s)\n')
	if(ncov>0){
		for (j in 1:ncov){
			tmp1 <- as.factor(as.matrix(mod0)[,j])
			design <- build.design(tmp1,des=design)
        }
    }
	if(!is.null(numCov)) design = cbind(design,theNumCov)
	return(design)
    
}