summariseByFeatures: Summarize by features

In LTLA/fugi: Further Utilities for Genomic Interactions

Description

Compute summary statistics of interactions for a given feature set. This includes the number of interactions (the sum of all interaction counts), number of unique interactions and number of trans (i.e., 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 'GenomicInteractions'
summariseByFeatures(GIObject, features,
  feature.name, distance.method = "midpoint", annotate.self = FALSE)

Arguments

GIObject	An annotated GenomicInteractions object.
features	A GRanges object containing the feature set.
feature.name	String specifying the name of the feature set.
distance.method	String specifying the method for calculating distances between anchors, see ?calculateDistances.
annotate.self	Logical scalar indicating whether to annotate self interactions, i.e., where a feature in 'features' overlaps both anchors of an interaction.

Value

A data.frame with one line for each range in features.

Examples

data("hic_example_data")
hic_example_data <- updateObject(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")

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