bedr.merge.region {bedr}

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.org/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);

}