InteractionHelpers: Interaction Type Helpers

In ComputationalRegulatoryGenomicsICL/GenomicInteractions: Utilities for handling genomic interaction data

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.