R/bedr.snm.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)
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bedr.snm.region <- function(x, method = "lexicographical", distance = 0, list.names = TRUE, number = FALSE, check.zero.based = TRUE, check.chr = TRUE, check.valid = TRUE,  verbose = TRUE) {
	x <- bedr.sort.region(x, check.zero.based = check.zero.based, check.chr = check.chr, check.valid = check.valid,  check.merge = F, verbose = verbose);
	x <- bedr.merge.region(x, distance = distance, list.names = list.names, number = number, check.zero.based = check.zero.based, check.chr = check.chr, check.valid = check.valid,  check.sort = F, verbose = verbose);
	return(x);
	}