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

In GenomicInteractions: Utilities for handling genomic interaction data

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')

GenomicInteractions documentation built on Nov. 8, 2020, 8:19 p.m.