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

In rBiopaxParser: Parses BioPax files and represents them in R

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.

Author(s)

fkramer

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

rBiopaxParser documentation built on Nov. 8, 2020, 8:21 p.m.