addPhysicalEntity {rBiopaxParser} | R Documentation |
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.
addPhysicalEntity( biopax, class = c("dna", "rna", "protein", "smallMolecule", "complex")[1], NAME, id = NULL, ORGANISM = NULL, COMMENT = NULL )
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 |
Returns the biopax model with the added physical entity.
fkramer
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