subsetByFeatures: Subset a GenomicInteractions object by features

In LTLA/fugi: Further Utilities for Genomic Interactions

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 'GenomicInteractions,GRanges,missing'
subsetByFeatures(GIObject,
  features, feature.class = NULL)


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


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

Arguments

GIObject	A GenomicInteractions object.
features	A GRanges or GRangesList object, or a character vector containing IDs of annotated features, e.g. promoter IDs.
feature.class	String containing the feature name to use if features is a character vector.

Value

A subsetted GenomicInteractions object.

Examples

data("hic_example_data")
hic_example_data <- updateObject(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")

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