getters: Functions to access data in a GenomicInteractions object

In LTLA/fugi: Further Utilities for Genomic Interactions

Description

These functions can be used to access data stored in the slots of a GenomicInteractions object. They are mostly retained for convenience and backwards compatibility - users are recommended to use the getters from the GenomicInteractions package itself.

Usage

name(GIObject)

anchorOne(GIObject)

anchorTwo(GIObject)

interactionCounts(GIObject)

annotationFeatures(GIObject)

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

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

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

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

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

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

## S4 method for signature 'GenomicInteractions'
seqinfo(x)

Arguments

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

Value

For anchorOne and anchorTwo, a GRanges for the first and second anchor regions, respectively.

For interactionCounts, a numeric vector with counts for each interaction in the object.

For description and name, a string containing the description and name of the object, respectively.

For annotationFeatures, a character vector of features with which the object was previously annotated, or NA if the object is unannotated.

For seqinfo, a Seqinfo object for the regions in GIObject.

Author(s)

Malcolm Perry, Elizabeth Ing-Simmons

Examples

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)

LTLA/fugi documentation built on June 22, 2019, 8:50 p.m.