getters: Functions to access data held in a GenomicInteractions...

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

Functions to access data held in a GenomicInteractions object.

Description

Use these functions to access data stored in each of the slots of a GenomicInteractions object.

Usage

name(GIObject)

anchorOne(GIObject)

anchorTwo(GIObject)

interactionCounts(GIObject)

annotationFeatures(GIObject)

## S4 method for signature 'GInteractions'
name(GIObject)

## S4 method for signature 'GInteractions'
description(object)

## S4 method for signature 'GInteractions'
anchorOne(GIObject)

## S4 method for signature 'GInteractions'
anchorTwo(GIObject)

## S4 method for signature 'GInteractions'
interactionCounts(GIObject)

## S4 method for signature 'GInteractions'
annotationFeatures(GIObject)

Arguments

GIObject	A Gnteractions object
object	Object, possibly derived from class eSet-class.

Value

For 'anchorOne' and 'anchorTwo', a GRanges. For 'interactionCounts', a numeric vector with counts for each interaction in the object. For 'description' and 'name', a character vector with length 1. For 'annotationFeatures', a character vector of features with which the object was previously annotated, or 'NA' if the object is unannotated.

Examples

library(GenomicRanges)

anchor.one = GRanges(c('chr1', 'chr1', 'chr1', 'chr1'), IRanges(c(10, 20, 30, 20), width=5))
anchor.two = GRanges(c('chr1', 'chr1', 'chr1', 'chr2'), IRanges(c(100, 200, 300, 50), width=5))
interaction_counts = sample(1:10, 4)
test <- GenomicInteractions(anchor.one, anchor.two, counts=interaction_counts)

name(test)
description(test)
anchorOne(test)
anchorTwo(test)
interactionCounts(test)

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