is.pp {GenomicInteractions} | R Documentation |
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:
promoter
distal
terminator
"is.trans" & "is.cis" select trans-chromosomal and intra-chromosomal interactions, respectively
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)
GIObject |
A GInteractions object |
x, y |
Names of annotated node classes |
A logical vector
data(hic_example_data) table(is.cis(hic_example_data)) sum(interactionCounts(hic_example_data))