summariseByFeatures {GenomicInteractions} | R Documentation

## Summary statistics of interactions for a given feature set

### Description

This function will calculate summary statistics for each element in the given feature set, including the number of interactions (the sum of all interaction counts), number of unique interactions and number of trans- (interchromosomal) interations. It also returns some statistics for the distances of interactions for all interactions of the feature, and for the different interaction types e.g. promoter-distal.

### Usage

    summariseByFeatures(GIObject, features, feature.name,
      distance.method = "midpoint", annotate.self = FALSE)

    ## S4 method for signature 'GInteractions'
    summariseByFeatures(GIObject, features, feature.name,
      distance.method = "midpoint", annotate.self = FALSE)

### Arguments

`GIObject` | An annotated GInteractions object
`features` | A GRanges object containing the feature set
`feature.name` | The name of the feature set
`distance.method` | Method for calculating distances between anchors, see ?calculateDistances
`annotate.self` | Logical. Indicates whether to annotate self interactions, i.e. where a feature in 'features' overlaps both anchors of an interaction. Default: FALSE.

### Value

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

### Examples

    data("hic_example_data")
    data("mm9_refseq_promoters")
    annotateInteractions(hic_example_data, list(promoter = mm9_refseq_promoters))
    summariseByFeatures(hic_example_data, mm9_refseq_promoters[1:10], "promoter")

[Package GenomicInteractions version 1.14.0 Index]