GenomicInteractions (version 1.6.2)

is.pp: 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)
"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)

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))