InteractionHelpers: Interaction type helper functions

In LTLA/fugi: Further Utilities for Genomic Interactions

Description

Functions to classify interactions within GenomicInteractions objects.

Usage

is.pp(GIObject)

is.pd(GIObject)

is.pt(GIObject)

is.dd(GIObject)

is.dt(GIObject)

is.tt(GIObject)

isInteractionType(GIObject, x, y)

is.trans(GIObject)

is.cis(GIObject)

## S4 method for signature 'GenomicInteractions'
is.pp(GIObject)

## S4 method for signature 'GenomicInteractions'
is.pd(GIObject)

## S4 method for signature 'GenomicInteractions'
is.pt(GIObject)

## S4 method for signature 'GenomicInteractions'
is.dd(GIObject)

## S4 method for signature 'GenomicInteractions'
is.dt(GIObject)

## S4 method for signature 'GenomicInteractions'
is.tt(GIObject)

## S4 method for signature 'GenomicInteractions'
isInteractionType(GIObject, x, y)

## S4 method for signature 'GenomicInteractions'
is.trans(GIObject)

## S4 method for signature 'GenomicInteractions'
is.cis(GIObject)

Arguments

GIObject	A GenomicInteractions object.
x, y	Names of annotated node classes

Details

isInteractionType identifies all interactions that occur between the annotated node classes x and y.

is.trans and is.cis select trans-chromosomal and intra-chromosomal interactions, respectively.

The other functions are convenience wrappers for identifying interactions between regions of common annotations, namely promoter p, distal d or terminator t regions.

Value

A logical vector indicating whether each entry of GIObject is of the specified type.

Author(s)

Malcolm Perry, Elizabeth Ing-Simmons

Examples

data(hic_example_data)
hic_example_data <- updateObject(hic_example_data)
table(is.cis(hic_example_data))
sum(interactionCounts(hic_example_data))

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