grow.region: Get adjacent flanks from regions

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

Get adjacent flanks from regions

Description

Get adjacent flanks from regions

Usage

grow.region(
	x,
	n.add = NULL,
	start.add = NULL,
	end.add = NULL,
	species = "human",
	build = "hg19",
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Arguments

x	a object region object or index
n.add	the number of bases to be selected from each side of a region
start.add	the number of based to be selected from the start of a region
end.add	the number of based to be selected from the end of a region
species	the species i.e. human or mouse
build	the genome build i.e. hg19 or mm10
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
check.merge	should overlapping regions be checked
verbose	should log messages and checking take place

Author(s)

Daryl Waggott

References

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

Examples

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

index <- get.example.regions();

a <- index[[1]];
a <- bedr(engine = "bedtools", input = list(i = a), method = "sort", params = "");
b <- grow.region(a, n.add = 20);

}

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