getNeighborhood {rBiopaxParser} | R Documentation |
This function searches the supplied biopax for interactions that are connected to the molecule or within 'depth' number of steps from it.
getNeighborhood(biopax, id, depth = 1, onlyInPathways = c(), biopaxlevel = 3)
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. |
Returns ids of interactions within 'depth' number of steps of the specified physicalEntity
fkramer