rBiopaxParser (version 2.10.0)

getNeighborhood: This function returns the neighborhood of a physicalEntity

Description

This function searches the supplied biopax for interactions that are connected to the molecule or within 'depth' number of steps from it.

Usage

getNeighborhood(biopax, id, depth = 1, onlyInPathways = c(), biopaxlevel = 3)

Arguments

biopax

A biopax model

id

string. ID of a physicalEntity (dna, rna, protein, complex, smallMolecule)

depth

integer. Search depth, this specifies how far out from the specified molecule the neighborhood should be streched.

onlyInPathways

character vector of pathway IDs. Search only in these pathways for neighbors.

biopaxlevel

integer. Set the biopax level here if you supply a data.table directly.

Value

Returns ids of interactions within 'depth' number of steps of the specified physicalEntity