bedr (version 1.0.2)

flank.region: Get adjacent flanks from regions

Description

Get adjacent flanks from regions

Usage

flank.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

References

http://bedtools.readthedocs.org/en/latest/content/tools/flank.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 <- flank.region(a, n.add = 20);

}