bedr.snm.region: sort a region file

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

Description

Sort and merge regions object in one step

Usage

bedr.snm.region(
	x,
	method = "lexicographical",
	distance = 0,
	list.names = TRUE,
	number = FALSE,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	verbose = TRUE
	)

Arguments

x	a object region object or index
method	natural or lexicographic
distance	distance between regions to be merged
list.names	output list of names for merged items
number	output number of merged items
check.zero.based	should 0 based coordinates be checked
check.chr	should chr prefix be checked
check.valid	should the region be checkded for integerity
verbose	should log messages and checking take place

Value

Sorted and merged regions object

Author(s)

Daryl Waggott

Examples

if (check.binary("bedtools")) {

index <- get.example.regions();

a <- index[[1]];

b <- bedr.snm.region(a);

}

bedr documentation built on May 2, 2019, 11:36 a.m.