calculateDistances {GenomicInteractions} | R Documentation

## Calculate interaction distances

### Description

This function takes a GInteractions object and calculates the distances between the anchors according to the value of `method`. The distances returned follow the same convention as distance(x, y) in GenomicRanges where the distance between adjacent regions is 0. Note that if anchors are overlapping this method will print a warning and return the distance as 0.

### Usage

    calculateDistances(GIObject, method = "midpoint", floor = TRUE)

    ## S4 method for signature 'GInteractions'
    calculateDistances(GIObject, method = "midpoint", floor = TRUE)

### Arguments

`GIObject` | A GInteractions object
`method` | Character vector indicating how to calculate distances, must be one of ‘midpoint’, ‘outer’, ‘inner’.
`floor` | A logical specifying whether to round down distances to nearest base pair or not. Default TRUE.

### Value

An vector containing the distances between anchors/GRanges, NA if on different chromosomes, rounded down to the nearest bp.

### Examples

    library(GenomicRanges)

    anchor.one <- GRanges(c('chr1', 'chr1', 'chr1', 'chr1'),
      IRanges(c(10, 20, 30, 20), width = 5))
    anchor.two <- GRanges(c('chr1', 'chr1', 'chr1', 'chr2'),
      IRanges(c(100, 200, 300, 50), width = 5))
    interaction_counts <- sample(1:10, 4)
    test <- GenomicInteractions(anchor.one, anchor.two, experiment_name = 'test',
                               description = 'this is a test',
                               counts = interaction_counts)
    calculateDistances(test, method = 'midpoint')

[Package GenomicInteractions version 1.28.0 Index]