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 1.14.0 Index]