rBiopaxParser (version 2.10.0)

addPathwayComponents: This function adds pathway components to an existing pathway

Description

This function adds pathway components to an existing pathway. Property PATHWAY-COMPONENTS are references to IDs of interaction/pathways/pathwaySteps (or subclasses of those)

Usage

addPathwayComponents(biopax, id, PATHWAY_COMPONENTS = c())

Arguments

biopax

A biopax model

id

string. ID for the pathway

PATHWAY_COMPONENTS

character vector. IDs of the pathway components. This must be IDs of instances of type interaction/pathway/pathwayStep (or their subclasses).

Value

Returns the biopax model with the pathway components added to the 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 = addPhysicalEntity(biopax, class="protein", id="p_id3", NAME="controllerProtein1")
biopax = addPhysicalEntityParticipant(biopax, "p_id3", id="PEP_p_id3")
biopax = addControl(biopax, CONTROL_TYPE="ACTIVATION", CONTROLLER="PEP_p_id3", CONTROLLED="biochem_id_1", id="c_id1")
biopax = addPathway(biopax, NAME="mypathway1", PATHWAY_COMPONENTS=c(), id="pw_id1")
biopax = addPathwayComponents(biopax, id="pw_id1", PATHWAY_COMPONENTS=c("c_id1"))
biopax$dt