GenomicInteractions-class: A S4 class to represent interactions between genomic regions.

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

A S4 class to represent interactions between genomic regions.

Description

@slot metadata List, defaults to 'experiment_name' and 'description', inherited from S4Vectors::Vector @slot anchor_one,anchor_two GRanges. Set of anchors of interactions. @slot counts integer vector, contains raw counts @slot elementMetadata DataFrame

This class is used to store information on which genomic regions are interacting with each other. Objects of this class contain information of the genomic coordinates of the interacting regions and the strength of these interactions, and associated metadata such as the name of the dataset and a brief description of the dataset. Interacting regions are stored as a pair of GenomicRanges: each set of anchor regions is stored as a separate GenomicRanges object, accessed by getAnchorOne and getAnchorTwo.

Examples

showClass('GenomicInteractions')
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)

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