getNeighborhood: This function returns the neighborhood of a physicalEntity

In frankkramer-lab/rBiopaxParser: Parses BioPax files and represents them in R

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

Author(s)

fkramer

frankkramer-lab/rBiopaxParser documentation built on July 19, 2020, 9:49 a.m.