valr (version 0.5.0)

bed_projection: Projection test for query interval overlap.

Description

Projection test for query interval overlap.

Usage

bed_projection(x, y, genome, by_chrom = FALSE)

Arguments

x

tbl_interval()

y

tbl_interval()

genome

tbl_genome()

by_chrom

compute test per chromosome

Value

tbl_interval() with the following columns:

• chrom the name of chromosome tested if by_chrom = TRUE, otherwise has a value of whole_genome

• p.value p-value from a binomial test. p-values > 0.5 are converted to 1 - p-value and lower_tail is FALSE

• obs_exp_ratio ratio of observed to expected overlap frequency

• lower_tail TRUE indicates the observed overlaps are in the lower tail of the distribution (e.g., less overlap than expected). FALSE indicates that the observed overlaps are in the upper tail of the distribution (e.g., more overlap than expected)

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

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002529

Other interval statistics: bed_absdist, bed_fisher, bed_jaccard, bed_reldist

Examples

# NOT RUN {
genome <- read_genome(valr_example('hg19.chrom.sizes.gz'))

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

bed_projection(x, y, genome)

bed_projection(x, y, genome, by_chrom = TRUE)

# }