R/create.tmp.bed.file.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
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create.tmp.bed.file <- function(x, name = "bedr", tmpDir = NULL) {
	old.scipen <- getOption("scipen")
	options(scipen = 999);

	tmpDir         <- ifelse (is.null(tmpDir), tempdir(), tmpDir);
	file.x         <- tempfile(pattern = paste(name, "_", sep = ""), tmpdir = tmpDir, fileext = ".bed");
	colnames(x)[1] <- paste("#",colnames(x)[1], sep="");
	write.table(x, file.x, quote = FALSE, row.names = FALSE, sep = "\t", col.names = FALSE);

	options(scipen = old.scipen)
	attr(file.x,"is.index") <- attr(x,"is.index");
	return(file.x);
	}