bedr.sort.region: sort a region file

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

Description

sort a region file

Usage

bedr.sort.region(
	x,
	method = "lexicographical",
	engine = "R",
	chr.to.num = c("X" = 23, "Y" = 24, "M" = 25),
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Arguments

x	a region object or index
method	natural or lexicographic
engine	what analytical engine to use for sorting i.e. bedtools, bedops, gnu unix
chr.to.num	chromosome letter names to numbers map. Defaults to Homo sapiens i.e c("X" = 23, "Y" = 24, "M" = 25)
check.zero.based	should 0 based coordinates be checked
check.chr	should chr prefix be checked
check.valid	should the region be checked for integerity
check.merge	should overlapping regions be checked
verbose	should log messages and checking take place

Author(s)

Daryl Waggott

References

http://bedtools.readthedocs.org/en/latest/content/tools/sort.html

Examples

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

index <- get.example.regions();
a <- index[[1]];
b <- bedr.sort.region(a);

}

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