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
Examples
Run this codedata(hic_example_data)
table(is.cis(hic_example_data))
sum(interactionCounts(hic_example_data))
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