R/order.region.R

In uclahs-cds/public-R-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.
# OICR makes no representations whatsoever as to the SOFTWARE contained herein.  It is experimental in nature and is provided WITHOUT
# WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. OICR MAKES NO REPRESENTATION
# OR WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT.
# By downloading this SOFTWARE, your Institution hereby indemnifies OICR against any loss, claim, damage or liability, of whatsoever kind or
# nature, which may arise from your Institution's respective use, handling or storage of the SOFTWARE.
# If publications result from research using this SOFTWARE, we ask that the Ontario Institute for Cancer Research be acknowledged and/or
# credit be given to OICR scientists, as scientifically appropriate.

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));
	}