is.pp {GenomicInteractions} | R 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))

[Package GenomicInteractions version 1.26.0 Index]