rBiopaxParser (version 2.10.0)

addBiochemicalReaction: This function adds a new biochemical reaction to the biopax model.

Description

This function adds a new biochemical reaction of class biochemicalReaction to the biopax model. This is a convenience function, internally the function addBiopaxInstance is called with properties LEFT and RIGHT set.

Usage

addBiochemicalReaction(biopax, LEFT = c(), RIGHT = c(), id = NULL)

Arguments

biopax

A biopax model

LEFT

vector of strings. IDs of the physicalEntityParticipant instances that are on the left side of this reaction.

RIGHT

vector of strings. IDs of the physicalEntityParticipant instances that are on the right side of this reaction.

id

string. ID for the control. If NULL a new ID is generated with prefix "biochemicalReaction".

Value

Returns the biopax model with the added pathway.

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_id_1")
biopax$dt