bed_jaccard {valr}

Calculate the Jaccard statistic for two sets of intervals.

Description

Quantifies the extent of overlap between to sets of intervals in terms of base-pairs. Groups that are shared between input are used to calculate the statistic for subsets of data.

Usage

bed_jaccard(x, y)

Arguments

x

ivl_df

y

ivl_df

Details

The Jaccard statistic takes values of ⁠[0,1]⁠ and is measured as:

J(x,y) = \frac{\mid x \bigcap y \mid} {\mid x \bigcup y \mid} = \frac{\mid x \bigcap y \mid} {\mid x \mid + \mid y \mid - \mid x \bigcap y \mid}

Interval statistics can be used in combination with dplyr::group_by() and dplyr::do() to calculate statistics for subsets of data. See vignette('interval-stats') for examples.

Value

tibble with the following columns:

• len_i length of the intersection in base-pairs

• len_u length of the union in base-pairs

• jaccard value of jaccard statistic

• n_int number of intersecting intervals between x and y

If inputs are grouped, the return value will contain one set of values per group.

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/jaccard.html

Other interval statistics: bed_absdist(), bed_fisher(), bed_projection(), bed_reldist()

Examples

genome <- read_genome(valr_example("hg19.chrom.sizes.gz"))

x <- bed_random(genome, seed = 1010486)
y <- bed_random(genome, seed = 9203911)

bed_jaccard(x, y)

# calculate jaccard per chromosome
bed_jaccard(
  dplyr::group_by(x, chrom),
  dplyr::group_by(y, chrom)
)