bedr (version 1.0.2)

bedr.join.multiple.region: join multiple region objects

Description

join multiple objects

Usage

bedr.join.multiple.region(
	x = list(),
	fraction.overlap = 1/1e9,
	empty = FALSE,
	missing.values = ".",
	cluster = FALSE,
	species = "human",
	build = "hg19",
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Arguments

x

list of region objects

fraction.overlap

proportion of bases to be considered an overlap

empty

print rows if no match

missing.values

missing value character

cluster

TRUE/FALSE for clustering

species

species i.e. human or mouse

build

genome build to use for empty regions

check.zero.based

should 0 based coordinates be checked

check.chr

should chr prefix be checked

check.valid

check if region is valid

check.sort

check if region is sorted

check.merge

check if overlapping regions are merged

verbose

messages and checks

References

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

Examples

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

index <- get.example.regions();

a <- index[[1]];
b <- index[[2]];

a.sort <- bedr.sort.region(a);
b.sort <- bedr.sort.region(b);
d <- get.random.regions(100, chr="chr1", sort = TRUE);

a.mult <- bedr.join.multiple.region(x = list(a.sort,b.sort,bedr.sort.region(d)));
}