bedr (version 1.0.2)

jaccard: calculate the jaccard distance between sets of intervals

Description

calculate the jaccard distance between sets of intervals

Usage

jaccard(
	x,
	y,
	proportion.overlap = 1e-09,
	reciprocal.overlap = FALSE,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Arguments

x

first region to be compared

y

second region to be compared

proportion.overlap

Defaults 1e-9 which is 1 bp. See details below for the different interpretation between 0 and 1 based overlap

reciprocal.overlap

Should the proportion.overlap be reciprocal

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

Value

A short vector.

Details

The Jaccard metric is the ratio of intersections to unions. The process can be tweaked by changing the proportion of overlap and even growiwng the regions.

References

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

See Also

reldist

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 = "");
jaccard(a,b);

}