Fisher's test to measure overlap between two sets of intervals.
Source:R/bed_fisher.r
bed_fisher.Rd
Calculate Fisher's test on number of intervals that are shared and unique
between two sets of x
and y
intervals.
Details
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.
See also
https://bedtools.readthedocs.io/en/latest/content/tools/fisher.html
Other interval statistics:
bed_absdist()
,
bed_jaccard()
,
bed_projection()
,
bed_reldist()
Examples
genome <- read_genome(valr_example("hg19.chrom.sizes.gz"))
x <- bed_random(genome, n = 1e4, seed = 1010486)
y <- bed_random(genome, n = 1e4, seed = 9203911)
bed_fisher(x, y, genome)
#> # A tibble: 1 × 6
#> estimate p.value conf.low conf.high method alternative
#> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
#> 1 0.945 0.707 0.722 1.22 Fisher's Exact Test for Count… two.sided