summariseByFeaturePairs: Summarise by feature pairs

In LTLA/fugi: Further Utilities for Genomic Interactions

Description

Calculat the number of interactions between two user-provided sets of features. This allows the summarisation of the number of features of a specific type that a particular region is involved in, and how many interactions exist between those features.

Usage

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

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

Arguments

GIObject	An annotated GenomicInteractions object.
features.one	A GRanges object containing the feature set of interest.
feature.name.one	String containing the name of the first feature set of interest.
features.two	A GRanges object containing the second feature set of interest.
feature.name.two	String containing the name of the second feature set of interest.

Value

A data.frame with one line for each combination of features.one and features.two.

Examples

data("hic_example_data")
hic_example_data <- updateObject(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
regs <- regions(hic_example_data, type=1)
p <- unique(unlist(head(regs$promoter.id)))
e <- unique(unlist(head(regs$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")

LTLA/fugi documentation built on June 22, 2019, 8:50 p.m.