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Calculate inter-region distances for genomic rainfall plots

Source: R/genomic-helper.R
genomic_dist.Rd

This function computes distances between adjacent genomic regions, grouped by chromosome. Useful for visualizing clustering or dispersion of genomic features.

Usage

genomic_dist(region, mode = NULL)

Arguments

region

A data frame with at least 3 columns: chromosome, start, and end.

mode

How to assign distance for intermediate regions: one of "min", "max", "mean", "left", or "right".

Value

A data frame with an additional dist column.

Details

The distance between two adjacent regions is calculated as the number of bases between the end position of the upstream region and the start position of the downstream region. If two regions overlap or are adjacent (<=1 bp apart), the distance is set to 0. The resulting distance is assigned to each region according to the selected mode:

  • "left": assign the distance to the upstream region

  • "right": assign to the downstream region

  • "min" / "max" / "mean": for intermediate regions, calculate the minimum, maximum, or average of the distances to neighboring regions