bedr (version 1.0.7)

bedr.subtract.region: subtracts features or ranges in object b from object a

Description

subtracts features or ranges in object b from object a

Usage

bedr.subtract.region(
	x,
	y,
	fraction.overlap = 1/1e9,
	remove.whole.feature = TRUE,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Value

Regions exclusive to one object of regions.

Arguments

x

item a

y

item b

fraction.overlap

what portion of A to be considered an overlap

remove.whole.feature

should whole feature be removed

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

check if region is sorted

check.merge

check if overlapping regions are merged

verbose

messages and checks

Author

Daryl Waggott

References

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

Examples

if (check.binary("bedtools")) {
index <- get.example.regions();

a <- index[[1]];
b <- index[[2]];
a <- bedr(engine = "bedtools", input = list(i = a), method = "sort", params = "");
b <- bedr(engine = "bedtools", input = list(i = b), method = "sort", params = "");
d <- bedr.subtract.region(a,b);
}