R/in.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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in.region <- function(x,y, proportion.overlap = 1e-9, reciprocal.overlap = FALSE, check.zero.based = TRUE, check.chr = TRUE, check.valid = TRUE, check.sort = TRUE, check.merge = TRUE, verbose = FALSE) {

	catv("REGION %in% REGION\n");

	reciprocal.overlap <- ifelse (reciprocal.overlap, "-r", "");
	params <- paste0("-c -f ", proportion.overlap, reciprocal.overlap)

	xy <- bedr(engine = "bedtools", 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);

	in.region <- xy[,ncol(xy)] > 0;
	
	return(in.region);
	}

`%in.region%` <- function(x,y) {
	in.region(x,y);
	}