R/bedr.subtract.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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bedr.subtract.region <- function(x, y, fraction.overlap = 1/1e9, remove.whole.feature = TRUE, check.zero.based = TRUE, check.chr = TRUE, check.valid = TRUE, check.sort = TRUE, check.merge = TRUE, verbose = TRUE) {
	catv("SUBTRACTING\n");

	fraction.overlap     <- ifelse(fraction.overlap == 1/1e9, "", paste("-f ", fraction.overlap));
	remove.whole.feature <- ifelse(remove.whole.feature, " -A ", "");
	xy <- bedr(engine = "bedtools", input = list(a = x, b = y), method = "subtract", params = paste(fraction.overlap, remove.whole.feature), 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);
	}