subsetByFeatures {GenomicInteractions}R Documentation

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")
annotateInteractions(hic_example_data, list(promoter = mm9_refseq_promoters))
ids <- names(mm9_refseq_promoters[1:10])
subsetByFeatures(hic_example_data, ids, "promoter")

[Package GenomicInteractions version 1.18.0 Index]