addPathwayComponents {rBiopaxParser} | R Documentation |
This function adds pathway components to an existing pathway. Property PATHWAY-COMPONENTS are references to IDs of interaction/pathways/pathwaySteps (or subclasses of those)
addPathwayComponents(biopax, id, PATHWAY_COMPONENTS = c())
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). |
Returns the biopax model with the pathway components added to the pathway
fkramer
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