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

In frankkramer-lab/rBiopaxParser: Parses BioPax files and represents them in R

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.

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 = 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

frankkramer-lab/rBiopaxParser documentation built on July 19, 2020, 9:49 a.m.