R/bedr.join.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
# (either version 1, or at your option, any later version) or the Artistic License 2.0.  Refer to LICENSE for the full license text.
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bedr.join.region <- function(x, y, fraction.overlap = 1/1e9, reciporical = FALSE, report.n.overlap = FALSE, check.zero.based = TRUE, check.chr = TRUE, check.valid = TRUE, check.sort = TRUE, check.merge = TRUE, verbose = TRUE) {

	catv("JOINING\n")

	if (report.n.overlap) {
		params <- "-wo -sorted"
		}
	else {
		params <- "-loj -sorted";
		}

	if (!check.sort || ! check.merge) {
		catv("  * bedr.join.region assumes sorted regions.\n    Also, overlapping regions cause unexpected results.\n")
		}

	xy <- bedr(
		input   = list(a = x, b = y),
		method  = 'intersect',
		params  = params, 
		check.zero.based = check.zero.based, check.chr = check.chr, check.valid = check.valid, check.sort = check.sort, check.merge = check.merge,
		verbose = verbose
		);

	return(xy);
	}