R/size.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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size.region <- function(x, zero.based = TRUE, check.zero.based = TRUE, check.chr = TRUE, check.valid = TRUE, verbose = TRUE) {

	x <- convert2bed(x, check.zero.based = check.zero.based, check.chr = check.chr, check.valid = check.valid, check.sort = FALSE, check.merge = FALSE, verbose = verbose);
	
	size <- x$end - x$start;
	if (!zero.based) size <- size + 1;
	
	return(size)
	}