rBiopaxParser (version 2.10.0)

addPhysicalEntityParticipant: This function adds a new physical entity participant.

Description

This function adds a new physical entity participant instance, which is a placeholder for physicalEntity class instances in interactions. This is a convenience function to add physicalEntityParticipant instances, internally the function addBiopaxInstance is called.

Usage

addPhysicalEntityParticipant(biopax, referencedPhysicalEntityID, id = NULL)

Arguments

biopax

A biopax model

referencedPhysicalEntityID

string. ID the new physicalEntity instance to reference here.

id

string. ID for the physical entity participant. If NULL a new ID is generated with prefix "physicalEntityParticipant".

Value

Returns the biopax model with the added physicalEntityParticipant.

Examples

biopax = createBiopax(level=2)
biopax = addPhysicalEntity(biopax, class="protein", id="p_id1", NAME="protein1")
biopax = addPhysicalEntityParticipant(biopax, "p_id1", id="PEP_p_id1")
biopax = addPhysicalEntity(biopax, class="protein", id="p_id2", NAME="protein2")
biopax = addPhysicalEntityParticipant(biopax, "p_id2", id="PEP_p_id2")
biopax = addBiochemicalReaction(biopax, LEFT=c("PEP_p_id1"), RIGHT=c("PEP_p_id2"), id="biochem_id1")
biopax$dt