R/cluster.region.R

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

# The bedr package is copyright (c) 2014 Ontario Institute for Cancer Research (OICR)
# This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
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cluster.region <- function(x, distance = 0, check.zero.based = TRUE, check.chr = TRUE, check.valid = TRUE, check.sort = TRUE, verbose = TRUE) {

catv("CLUSTERING\n")

	if (is.vector(x) || ncol(x)<4) {list.names=FALSE}

	if(is.vector(x, mode = "character")) {
		n.rec.before <- length(x)
		}
	else {
		n.rec.before <- nrow(x)
		}

	x <- bedr(engine = "bedtools", input = list(i = x), method = "cluster", params = paste("-d", distance), check.zero.based = check.zero.based, check.chr = check.chr, check.valid = check.valid, check.merge = FALSE, check.sort = check.sort, verbose = verbose);

	if(is.vector(x, mode = "character")) {
		n.rec.after <- length(unique(x[,2]));
		colnames(x)[2] <- "regionIndex";
		}
	else {
		n.rec.after <- length(unique(x[,ncol(x)]))
		colnames(x)[ncol(x)] <- "regionIndex";
		}

	catv(paste0("  * Collapsing ", n.rec.before, " --> ", n.rec.after, " regions... NOTE\n"))

	return(x);
	}