calculateDistances: Calculate interaction distances

In LTLA/fugi: Further Utilities for Genomic Interactions

Description

This computes the linear distances between anchoring regions for each interaction, simply by calling the pairdist function from GenomicInteractions.

Usage

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

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

Arguments

GIObject	A GenomicInteractions object
method	String indicating how to calculate distances. Should be "midpoint", "outer" or "inner".
floor	A logical specifying whether to round down distances to the nearest base pair. Defaults to TRUE.

Value

A numeric vector containing the distances between anchors/GRanges. If floor=TRUE, this vector is integer. Interactions on different chromosomes have distances set to NA.

Author(s)

Malcolm Perry, Elizabeth Ing-Simmons

See Also

pairdist, which this function calls.

Examples

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))
test <- GenomicInteractions(anchor.one, anchor.two)
calculateDistances(test, method="midpoint")
        

LTLA/fugi documentation built on June 22, 2019, 8:50 p.m.