viewPoint: Virtual 4C viewpoint

In LTLA/fugi: Further Utilities for Genomic Interactions

Description

Create a GenomicInteractions object with interactions originating at a given “bait” viewpoint, or a set of such 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 GenomicInteractions object.
bait	A GRanges object describing bait regions.
region	An optional GRanges object specifying the region to look for bait interactions in.
...	Additional arguments to pass to findOverlaps.

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.

Value

A GenomicInteractions object.

Examples

data(hic_example_data)
hic_example_data <- updateObject(hic_example_data)

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)

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