summariseByFeatures: Summary statistics of interactions for a given feature set

Description Usage Arguments Value Examples

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

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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

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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")

Bioconductor-mirror/GenomicInteractions documentation built on June 23, 2017, 6:23 p.m.