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 1.12.1 Index]