summariseByFeaturePairs {GenomicInteractions} | R Documentation

## Summarise the number of interactions between two sets of features.

### Description

This function will calculate the number of observed interactions between two sets of features provided by the end-user. This allows the summarisation of the number of features of a specific type a particular region is involved in and how many interactions exist between them.

### Usage

    summariseByFeaturePairs(GIObject, features.one, feature.name.one, features.two,
      feature.name.two)

    ## S4 method for signature 'GInteractions'
    summariseByFeaturePairs(GIObject, features.one,
      feature.name.one, features.two, feature.name.two)

### Arguments

`GIObject` | An annotated GInteractions object
`features.one` | A GRanges object containing the feature set of interest
`feature.name.one` | The name of the first feature set of interest
`features.two` | A GRanges object containing the second feature set of interest
`feature.name.two` | The name of the second feature set of interest

### Value

A data frame with one line for each range in ‘features’

### Examples

    data("hic_example_data")
    data("mm9_refseq_promoters")
    data("thymus_enhancers")
    annotateInteractions(hic_example_data, list(promoter = mm9_refseq_promoters, enhancer = thymus_enh))
    # can be slow so subset of features used for examples
    p <- unique(unlist(head(regions(hic_example_data)$promoter.id)))
    e <- unique(unlist(head(regions(hic_example_data)$enhancer.id)))
    p <- p[!is.na(p)]
    p <- mm9_refseq_promoters[p]
    e <- e[!is.na(e)]
    e <- thymus_enh[e]
    ep_summary <- summariseByFeaturePairs(hic_example_data, p, "promoter", e, "enhancer")

[Package GenomicInteractions version 1.14.0 Index]