GInteractions-subsetByFeatures-methods: Subset a GInteractions object by features

In ComputationalRegulatoryGenomicsICL/GenomicInteractions: Utilities for handling genomic interaction data

Subset a GInteractions object by features

Description

Subsets interactions for which at least one of the anchors overlaps with a given GRanges object. Alternatively, subsets interactions based on annotated feature IDs for a particular feature.

Usage

subsetByFeatures(GIObject, features, feature.class = NULL)

## S4 method for signature 'GInteractions,GRanges,missing'
subsetByFeatures(GIObject, features, feature.class = NULL)

## S4 method for signature 'GInteractions,GRangesList,missing'
subsetByFeatures(GIObject, features, feature.class = NULL)

## S4 method for signature 'GInteractions,character,character'
subsetByFeatures(GIObject, features, feature.class = NULL)

Arguments

GIObject	A GInteractions object
features	A GRanges or GRangesList object, or a character vector containing IDs of annotated features, e.g. promoter IDs.
feature.class	If ‘features’ is a character vector, the corresponding feature name, e.g. 'promoter'.

Value

a subsetted GInteractions object

Examples

data('hic_example_data')
data('mm9_refseq_promoters')
ids <- names(mm9_refseq_promoters[1:10])
subsetByFeatures(hic_example_data, ids, 'promoter')

ComputationalRegulatoryGenomicsICL/GenomicInteractions documentation built on April 16, 2022, 4:09 a.m.