GenomicInteractions (version 1.6.2)

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