R/index2bed.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
# (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
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index2bed <- function(x, set.type = TRUE) {

	# check its vector
	if (!is.null(dim(x)) || !is.character(x)) {
		return(x);
		}

	# split the index
	index <- strsplit2matrix(x, split = ":|-");

	# add the colnames
	colnames(index) <- c("chr","start","end");
	index$start     <- suppressWarnings(as.numeric(index$start));
	index$end       <- suppressWarnings(as.numeric(index$end));

	if (set.type) attr(x, "input.type") <- 1;
	return(index);
	}