GOTerms-class {annotate}R Documentation

Class "GOTerms"

Description

A class to represent Gene Ontology terms for a given node

Objects from the Class

Objects can be created by calls of the form new("GOTerms", GOId, Term, Category, Synonym, Secondary, Definition). GOId, Term, and Category are required.

Slots

GOID:
Object of class "character" A character stirng for the GO id of a primary node
Term:
Object of class "character" A character string that defines the role of gene product corresponding to the primary GO id
Synonym:
Object of class "character" other ontology terms that are considered to be synonymous to the primary term attached to the GO id (e.g. type I programmed cell death is a synonym of apoptosis). Synonymous here can mean that the synonym is an exact synonym of the primary term, is related to the primary term, is broader than the primary term, is more precise than the primary term, or name is related to the term, but is not exact, broader or narrower.
Secondary:
Object of class "character" GO ids that are secondary to the primary GO id as results of merging GO terms so that One GO id becomes the primary GO id and the rest become the secondary
Definition:
Object of class "character" Further definition of the ontology of the primary GO id
Ontology:
Object of class "character" Gene Ontology category. Can be MF - molecular function, CC - cellular component, or BP - biological process

Methods

Ontology
signature(object = "GOTerms"): The get method for slot Ontology
Ontology
signature(object = "ANY"): The get method for slot Ontology handles missing values.
Definition
signature(object = "GOTerms"): The get method for slot Definition
GOID
signature(object = "GOTerms"): The get method for slot GOID
Term
signature(object = "GOTerms"): The get method for slot Term
Secondary
signature(object = "GOTerms"): The get method for slot Secondary
Synonym
signature(object = "GOTerms"): The get method for slot Synonym
print
signature(x = "GOTerms"): The method for pretty print

Note

GOTerms objects are used to represent GO terms for primary GO nodes in the annotation data package GO

Author(s)

Jianhua Zhang

References

http://www.geneontology.org/

Examples

  goTerms <- new("GOTerms", GOID = "GO:1234567", Term = "Test",
                 Ontology = "MF")
  GOID(goTerms)
  Term(goTerms)
  Ontology(goTerms)

[Package annotate version 1.8.0 Index]