bedr.merge.region: merge i.e. collapse overlpaping regions

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

merge i.e. collapse overlpaping regions

Description

merge i.e. collapse overlpaping regions

Usage

bedr.merge.region(
	x,
	distance = 0,
	list.names = TRUE,
	number = FALSE,
	stratify.by = NULL,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	verbose = TRUE
	);

Arguments

x	input
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.
list.names	output list of names for merged items
number	output number of merged items
stratify.by	a column name indicating the groups to stratify merging within i.e. gene name. merging will not happen between groups.
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 the sort order be checked
verbose	should log messages and checking take place

Author(s)

Daryl Waggott

References

http://bedtools.readthedocs.io/en/latest/content/tools/merge.html

Examples

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

index <- get.example.regions();

a <- index[[1]];

a.sort   <- bedr.sort.region(a);
a.merged <- bedr.merge.region(a.sort);

}

bedr documentation built on April 11, 2025, 5:52 p.m.