addPhysicalEntity: This function adds a new physical entity.

In rBiopaxParser: Parses BioPax files and represents them in R

Description

This function adds a new physical entity of chosen class to the biopax model. This is a convenience function to add physical entities, internally the function addBiopaxInstance is called with properties NAME and ORGANISM set.

Usage

addPhysicalEntity(
  biopax,
  class = c("dna", "rna", "protein", "smallMolecule", "complex")[1],
  NAME,
  id = NULL,
  ORGANISM = NULL,
  COMMENT = NULL
)

Arguments

biopax	A biopax model
class	string. Class of the physical entity to add, choose from c("dna","rna","protein","smallMolecule","complex").
NAME	string. Name of the new physical entity
id	string. ID for the physical entity. If NULL a new ID is generated with prefix "physicalEntity".
ORGANISM	string. Organism property of the molecule. optional.
COMMENT	string. An optional comment

Value

Returns the biopax model with the added physical entity.

Author(s)

fkramer

Examples

biopax = createBiopax(level=2)
biopax = addBiopaxInstance(biopax, class="protein", id="id1", properties=list(NAME="protein1",COMMENT="this is my first protein!"))
biopax$dt
biopax = addPhysicalEntity(biopax, class="protein", id="id2", NAME="protein2", COMMENT="This is a protein added using the convenience function addPhysicalEntitiy")
biopax$dt

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