bedr (version 1.0.2)

snm: sort a region file

Description

Sort and merge regions object in one step

Usage

snm(
	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 and regions object

Examples

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

index <- get.example.regions();

a <- index[[1]];

b <- snm(a);

}