bed_absdist: Compute absolute distances between intervals.

In jayhesselberth/valr: Genome Interval Arithmetic

Compute absolute distances between intervals.

Description

Computes the absolute distance between the midpoint of each x interval and the midpoints of each closest y interval.

Usage

bed_absdist(x, y, genome)

Arguments

x	ivl_df
y	ivl_df
genome	genome_df

Details

Absolute distances are scaled by the inter-reference gap for the chromosome as follows. For Q query points and R reference points on a chromosome, scale the distance for each query point i to the closest reference point by the inter-reference gap for each chromosome. If an x interval has no matching y chromosome, .absdist is NA.

d_i(x,y) = min_k(|q_i - r_k|)\frac{R}{Length\ of\ chromosome}

Both absolute and scaled distances are reported as .absdist and .absdist_scaled.

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

ivl_df with .absdist and .absdist_scaled columns.

See Also

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

Other interval statistics: bed_fisher(), bed_jaccard(), 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_absdist(x, y, genome)

jayhesselberth/valr documentation built on April 8, 2024, 12:32 p.m.