summariseByFeaturePairs: Summarise the number of interactions between two sets of...

summariseByFeaturePairsR 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')

ComputationalRegulatoryGenomicsICL/GenomicInteractions documentation built on April 16, 2022, 4:09 a.m.