R/order.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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order.region <- function(x, method = "lex", check.zero.based = TRUE, check.chr = TRUE, check.valid = TRUE, check.merge = TRUE) {
	x <- convert2bed(x, check.zero.based = check.zero.based, check.chr = check.chr, check.valid = check.valid, check.sort = FALSE, check.merge = check.merge);
	x <- data.frame(x, row.order = 1:nrow(x), stringsAsFactors = FALSE);
	x <- bedr.sort.region(x, method = method,check.zero.based = check.zero.based, check.chr = check.chr, check.valid = FALSE, check.merge = FALSE, verbose = FALSE);
	return(as.numeric(x$row.order));
	}