# 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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12``` ```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.

A short vector.

Daryl Waggott

reldist

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11``` ```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.