summariseByFeatures: Summary statistics of interactions for a given feature set

In ComputationalRegulatoryGenomicsICL/GenomicInteractions-new: Utilities for handling genomic interaction data

Summary statistics of interactions for a given feature set

Description

This function will calculate summary statistics for each element in the given feature set, including the number of interactions (the sum of all interaction counts), number of unique interactions and number of trans- (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 'GInteractions'
summariseByFeatures(
  GIObject,
  features,
  feature.name,
  distance.method = "midpoint",
  annotate.self = FALSE
)

Arguments

GIObject	An annotated GInteractions object
features	A GRanges object containing the feature set
feature.name	The name of the feature set
distance.method	Method for calculating distances between anchors, see ?calculateDistances
annotate.self	Logical. Indicates whether to annotate self interactions, i.e. where a feature in 'features' overlaps both anchors of an interaction. Default: FALSE.

Value

A data frame with one line for each range in ‘features’

Examples

data('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')

ComputationalRegulatoryGenomicsICL/GenomicInteractions-new documentation built on April 10, 2022, 5:39 p.m.