is.sorted.region: checks if region file is sorted

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

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);
}

bedr documentation built on April 11, 2025, 5:52 p.m.