rBiopaxParser (version 2.10.0)

addPathway: This function adds a new pathway to the biopax model.

Description

This function adds a new pathway + its PATHWAY-COMPONENTS (references to interaction/pathways/pathwaySteps)

Usage

addPathway(biopax, NAME, PATHWAY_COMPONENTS = c(), id = NULL, ORGANISM = NULL, COMMENT = NULL)

Arguments

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

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 = 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