GenomicInteractions (version 1.6.2)

viewPoint: Virtual 4C viewpoint

Description

This function creates a GInteractions object representing interactions originating at a given viewpoint ("bait"), or set of viewpoints. This is similar to the idea of a virtual 4C experiment where you are interested in interactions with a specific region.

Usage

viewPoint(x, bait, region = NULL, ...)

Arguments

x

A GInteractions object.

bait

A GRanges object describing bait regions.

region

If present, a GRanges object specifying the region to look for bait interactions in.

...

additional arguments to findoverlaps

Value

A GInteractions object.

Details

The object returned has the "bait" as anchor one, and the interacting regions as anchor two. By default this is genome wide. If you only want to consider interactions within a certain distance around the bait, you can specify a region to consider.

Multiple baits can be given, e.g. to find all interactions around promoters.

You may want to visualise the resulting interactions in a genome browser - you can do this by creating coverage over anchor two of the object and exporting as a wig or bedgraph file.

Examples

data(hic_example_data)
library(GenomicRanges)
pos <- GRanges(seqnames="chr15", ranges=IRanges(start=59477709, end=59482708))
region <- GRanges(seqnames="chr15", ranges=IRanges(start=58980209, end=59980208))
vp <- viewPoint(hic_example_data, pos, region)