addPathway {rBiopaxParser} | R Documentation |
This function adds a new pathway + its PATHWAY-COMPONENTS (references to interaction/pathways/pathwaySteps)
addPathway( biopax, NAME, PATHWAY_COMPONENTS = c(), id = NULL, ORGANISM = NULL, COMMENT = NULL )
biopax |
A biopax model |
NAME |
string. Name of 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). |
id |
string. ID for the pathway. If NULL a new ID is generated with prefix "pathway". |
ORGANISM |
string. Organism property of the pathway. optional. |
COMMENT |
string. An optional comment |
Returns the biopax model with the added 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("c_id1"), id="pw_id1") biopax$dt