bedr (version 1.0.7)

bedr.snm.region: sort a region file

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
	)

Value

Sorted and merged regions object

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

Author

Daryl Waggott

Examples

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

index <- get.example.regions();

a <- index[[1]];

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

}