R/assign.to.clusters.R

In PeteHaitch/Aclust: Clustering functions and analysis pipeline for methylation outcome data based on clustering and GEEs

assign.to.clusters <-
function(betas, annot = NULL, annotation.file.name = NULL, dist.type = "spearman", method = "single", dist.thresh = 0.5, bp.merge = 0, bp.thresh.clust = Inf, return.chroms = NULL){
### function that gets a matrix of beta values and returns a list of cluster assignments. it uses the
### function order.betas.by.chrom.location to order the data corresponding to each chromosome and 
### then applies the clustering algorithm	
## return the list ordered by the number of sites in the cluster
	
	chrom.list <- order.betas.by.chrom.location(betas, annot = annot, annotation.file.name = annotation.file.name, return.chroms = return.chroms)
	clusters.by.chrom <- vector(mode = "list", length = length(chrom.list[[1]]))
	
	
	for (i in 1:length(chrom.list[[1]])){
		betas.temp <- chrom.list[[1]][[i]]
		locations.temp <- chrom.list[[2]][[i]]
		
		betas.temp <- betas.temp[which(!is.na(locations.temp$Coordinate_36)),]
		locations.temp <- locations.temp[!is.na(Coordinate_36)]
		
		if (!is.null(bp.merge)) which.clust <- Dbp.merge(t(betas.temp), thresh.dist = dist.thresh, bp.thresh.dist = bp.merge, as.numeric(locations.temp$Coordinate_36),  dist.type = dist.type)
			else which.clust <- 1:nrow(locations.temp)
		if (!is.null(bp.thresh.clust))	
			clust.vec <- Acluster(t(betas.temp), thresh.dist = dist.thresh, which.clust = which.clust, location.vec = as.numeric(locations.temp$Coordinate_36), max.dist =  bp.thresh.clust, type = method, dist.type = dist.type)  else 
					clust.vec <- Acluster(t(betas.temp), thresh.dist = NULL, which.clust = which.clust, location.vec = NULL, max.dist =  bp.thresh.clust, type = method, dist.type = dist.type)

		clusters.by.chrom[[i]] <- lapply(clust.vec, function(x) return(locations.temp$IlmnID[which(clust.vec == x)]))
		clusters.by.chrom[[i]] <- clusters.by.chrom[[i]][which(!duplicated(clusters.by.chrom[[i]]))]
		
		if (i == 1) clusters.all <- clusters.by.chrom[[1]] 
			else clusters.all <- c(clusters.all, clusters.by.chrom[[i]])

	}
	
	return(clusters.all)
	
}