GOTerms-class {annotate} | R Documentation |
A class to represent Gene Ontology terms for a given node
Objects can be created by calls of the form new("GOTerms",
GOId, Term, Category, Synonym, Secondary, Definition)
.
GOId, Term, and Category are required.
GOID
:"character"
A character
stirng for the GO id of a primary nodeTerm
:"character"
A
character string that defines the role of gene product
corresponding to the primary GO idSynonym
:"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
:"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 secondaryDefinition
:"character"
Further
definition of the ontology of the primary GO idOntology
:"character"
Gene
Ontology category. Can be MF - molecular function, CC - cellular
component, or BP - biological processsignature(object = "GOTerms")
: The get method
for slot Ontologysignature(object = "ANY")
: The get method
for slot Ontology handles missing values.signature(object = "GOTerms")
: The get
method for slot Definitionsignature(object = "GOTerms")
: The get method for
slot GOIDsignature(object = "GOTerms")
: The get method
for slot Termsignature(object = "GOTerms")
: The get
method for slot Secondarysignature(object = "GOTerms")
: The get method
for slot Synonymsignature(x = "GOTerms")
: The method for pretty
printGOTerms objects are used to represent GO terms for primary GO nodes in the annotation data package GO
Jianhua Zhang
goTerms <- new("GOTerms", GOID = "GO:1234567", Term = "Test", Ontology = "MF") GOID(goTerms) Term(goTerms) Ontology(goTerms)