cluster.region {bedr}

cluster intervals

Description

cluster intervals

Usage

cluster.region(
	x,
	distance = 0,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	verbose = TRUE
	)

Arguments

x

The region

distance

maximum distance between regions to be merged. defaults to 0 which means overlapping or bookended features. note that you can use negative distances to enforce a minimum overlap.

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

check.sort

should regions be checked for sort order

verbose

should log messages and checking take place

Details

clusters adjacent features of a specified distance.

Value

A data.frame in bed format

Author(s)

Daryl Waggott

References

http://bedtools.readthedocs.org/en/latest/content/tools/cluster.html

See Also

bedr.merge.region

Examples

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

index <- get.example.regions();

a <- index[[1]];

b <- cluster.region(a, distance = 0);
d <- cluster.region(a, distance = 100);

}