addControl: This function adds a new control to the biopax model.

In rBiopaxParser: Parses BioPax files and represents them in R

Description

This function adds a new interaction of class control to the biopax model. This is a convenience function to add controls, internally the function addBiopaxInstance is called with properties CONTROL-TYPE, CONTROLLER and CONTROLLED set.

Usage

addControl(
  biopax,
  CONTROL_TYPE = c("ACTIVATION", "INHIBITION"),
  CONTROLLER = "",
  CONTROLLED = c(),
  id = NULL
)

Arguments

biopax	A biopax model
CONTROL_TYPE	string. Specifies wether this is an activating or inhibiting control.
CONTROLLER	string. ID of the physicalEntityParticipant instance that is the controller of this interaction.
CONTROLLED	vector of strings. IDs of the interaction and/or pathway instances that are being controlled.
id	string. ID for the control. If NULL a new ID is generated with prefix "control".

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$dt

rBiopaxParser documentation built on Nov. 8, 2020, 8:21 p.m.