findDistalAnchors: Find distal anchor regions

In LTLA/GenomicInteractions: Classes and Methods for Handling Genomic Interaction Data

Description

Given a reference region, find the distal anchor regions that interact with that region.

Usage

## S4 method for signature 'GenomicInteractions'
findDistalAnchors(x, ref, local = TRUE,
  ...)

Arguments

x	A GenomicInteractions object.
ref	A GenomicRanges object of length 1.
local	A logical scalar specifying whether interactions should be retained if both anchors overlap ref.
...	Further arguments to pass to findOverlaps.

Details

This function will identify all interactions in x that have one-dimensional overlaps with ref, and it will return the non-overlapping anchor region for each such interaction. Any per-interaction metadata in x is carried over to the output object, along with per-feature metadata in regions(x).

The returned genomic intervals represent the distal interactors to ref in x. One can view this as taking a “cross-section” of the interaction space at the specified ref, thus projecting all the interactions involving ref onto the linear genome. This is analogous to what is done in 4C experiments.

Value

A GenomicRanges object containing all distal anchor regions.

Author(s)

Aaron Lun

Examples

anchor1 <- GRanges("chr1", IRanges(sample(1000, 100), width=5))
anchor2 <- GRanges("chr1", IRanges(sample(1000, 100), width=5))
test <- GenomicInteractions(anchor1, anchor2)
mcols(test)$original <- seq_along(test)
test

findDistalAnchors(test, GRanges("chr1:1-100"))
findDistalAnchors(test, GRanges("chr1:1-100"), local=FALSE)
findDistalAnchors(test, GRanges("chr1:1-100"), type="within")

LTLA/GenomicInteractions documentation built on June 24, 2019, 2:09 p.m.