cluster.region: cluster intervals

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

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);

}

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