GenomicInteractions (version 1.6.2)

summariseByFeaturePairs: 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)
"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")