InteractionHelpers: Interaction Type Helpers

is.ppR Documentation

Interaction Type Helpers

Description

Functions to classify interactions within GInteractions objects.

  • 'isInteractionType' takes two character arguments which are annotated node classes and returns interactions between them.

  • 'is.pp', 'is.pd' etc. are bindings for common annotations:

    p

    promoter

    d

    distal

    t

    terminator

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

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 'GInteractions'
is.pp(GIObject)

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

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

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

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

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

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

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

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

Arguments

GIObject

A GInteractions object

x, y

Names of annotated node classes

Value

A logical vector

Examples

data(hic_example_data)
table(is.cis(hic_example_data))
sum(interactionCounts(hic_example_data))


ComputationalRegulatoryGenomicsICL/GenomicInteractions documentation built on April 16, 2022, 4:09 a.m.