annotateInteractions: Annotate the interactions in a GInteractions object

In ComputationalRegulatoryGenomicsICL/GenomicInteractions-new: Utilities for handling genomic interaction data

Annotate the interactions in a GInteractions object

Description

This function annotates the regions of a GInteractions object according to their overlaps with 'annotations', a list of named GRanges (or GRangesList) objects.

Usage

annotateInteractions(GIObject, annotations, id.col = NULL)

## S4 method for signature 'GInteractions,list'
annotateInteractions(GIObject, annotations, id.col = NULL)

Arguments

GIObject	A GInteractions object to be annotated
annotations	A list containing GRanges (or GRangesList) objects with which to annotate the GInteractions object.
id.col	Metadata column of GRanges objects to use as feature ID. Default: NULL.

Details

Metadata columns will be added to the regions of the GInteractions object, named according to the names of 'annotations' and containing the id(s) of the corresponding overlapping genomic interval(s). If 'annotations' is not named, the metadata columns will be named 'FEATURE#.id' where # is the position in the list.

IDs for features in each element of annotations will be extracted according to the following rules: if the annotation features are a GRanges object and a metadata column is specified using 'id.col', this column will be used as feature IDs. Otherwise, if the annotation features are named, their names will be used. If neither of these are present, they will be given numeric IDs.

For each anchor a 'node.class' metadata column will also be added, containing the name of the list element which was first annotated to each range. Ranges with no overlaps will be classified as 'distal'.

Value

invisible(1)

Examples

library('GenomicRanges')
data(hic_example_data)
data(mm9_refseq_promoters)
mm9_refseq_grl = split(mm9_refseq_promoters, mm9_refseq_promoters$id)
# This adds a `promoter.id` metadata column to regions(hic_example_data)
# containing IDs of overlapping promoters for each region, taken from
# names(mm9_refseq_grl)
annotateInteractions(hic_example_data, list(promoter=mm9_refseq_grl))

ComputationalRegulatoryGenomicsICL/GenomicInteractions-new documentation built on April 10, 2022, 5:39 p.m.