bedr (version 1.0.2)

bedr.join.region: join two region objects using a left outer join

Description

join two region objects using a left outer join

Usage

bedr.join.region(
	x,
	y,
	fraction.overlap = 1/1e9,
	reciporical = FALSE,
	report.n.overlap = FALSE,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Arguments

x

object a

y

object b

fraction.overlap

proportion of overlap to be considered a match

report.n.overlap

should the number of overlapping bases be reported

reciporical

should the fraction overlap be applied to object b as well

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/intersect.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 <- bedr.join.region(a.sort, b.sort);
}