jaccard: calculate the jaccard distance between sets of intervals

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

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

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.

Value

A short vector.

Author(s)

Daryl Waggott

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);

}

Example output

sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied


######################
#### bedr v1.0.3 ####
######################

checking binary availability...
  * Checking path for bedtools... FAIL
  * Checking path for bedops... FAIL
  * Checking path for tabix... FAIL
tests and examples will be skipped on R CMD check if binaries are missing

  * Checking path for bedtools... sh: 1: cannot create /dev/null: Permission denied
FAIL

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