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

	x.merge   <- bedr.merge.region(x, check.zero.based = check.zero.based, check.chr = check.chr, check.valid = check.valid, check.sort = check.sort, verbose = FALSE);
	if (is.vector(x)) {
		is.merged <- length(x) == length(x.merge);
		}
	else {
		if (is.null(nrow(x)) || is.null(nrow(x.merge))) {
			is.merged <- FALSE;
			}
		else {
			is.merged <- nrow(x) == nrow(x.merge);
			}
		}
	
	catv(" * Checking for overlapping 'contiguous' regions... ")
	if (is.merged) {
		catv("PASS\n");
		}
	else {
		catv("FAIL\n")
		catv(paste0("   The input for object has overlapping features!\n   This can cause unexpected results for some set operations.\n   i.e. x <- bedr.merge.region(x)\n", sep = ""));
		}

	return(is.merged);
	}