is.sorted.region {bedr}

checks if region file is sorted

Description

checks if region file is sorted

Usage

is.sorted.region(
	x,
	method = "lex",
	engine = "unix",
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.merge = TRUE,
	verbose = FALSE
	)

Arguments

x

The region index, bed file, or bed formatted object

method

lexicgraphical or natural, lex is required for many operations but natural is better for interpretation

engine

what analytical engine to use for sorting i.e. bedtools, bedops, gnu unix

check.zero.based

should 0 based coordinates be checked

check.chr

should chr prefix be checked

check.valid

check if region is valid

check.merge

check if region is merged

verbose

more words

Author(s)

Daryl Waggott

Examples

if (check.binary("bedtools")) {
index <- get.example.regions();

a <- index[[1]];

b <- is.sorted.region(a);
}