GenomicInteractions: Function to create a GenomicInteractions object

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

Function to create a GenomicInteractions object

Description

Create GenomicInteractions objects from two GRanges ojects.

Usage

GenomicInteractions(anchor1, anchor2, counts, ...)

## S4 method for signature 'GRanges,GRanges,numeric'
GenomicInteractions(anchor1, anchor2, counts, ...)

## S4 method for signature 'GInteractions,ANY,ANY'
GenomicInteractions(anchor1)

## S4 method for signature 'GInteractions,numeric,ANY'
GenomicInteractions(anchor1, anchor2)

## S4 method for signature 'numeric,numeric,GRanges'
GenomicInteractions(anchor1, anchor2, counts, ...)

## S4 method for signature 'GRanges,GRanges,GenomicRanges_OR_missing'
GenomicInteractions(anchor1, anchor2, counts, ...)

## S4 method for signature 'missing,missing,GenomicRanges_OR_missing'
GenomicInteractions(anchor1, anchor2, counts, ...)

## S4 method for signature 'ANY,ANY,ANY'
GenomicInteractions(anchor1, anchor2, counts, ...)

Arguments

anchor1, anchor2	GRanges objects.
counts	An integer vector, defaults to 1.
...	Additional data to be added to mcols

Value

a GenomicInteractions object

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)

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