\HeaderA{GOTerms-class}{Class "GOTerms"}{GOTerms.Rdash.class}
\aliasA{Definition}{GOTerms-class}{Definition}
\aliasA{Definition,GOTerms-method}{GOTerms-class}{Definition,GOTerms.Rdash.method}
\aliasA{GOID}{GOTerms-class}{GOID}
\aliasA{GOID,GOTerms-method}{GOTerms-class}{GOID,GOTerms.Rdash.method}
\aliasA{GOTerms}{GOTerms-class}{GOTerms}
\aliasA{Ontology}{GOTerms-class}{Ontology}
\aliasA{Ontology,ANY-method}{GOTerms-class}{Ontology,ANY.Rdash.method}
\aliasA{Ontology,GOTerms-method}{GOTerms-class}{Ontology,GOTerms.Rdash.method}
\aliasA{Secondary}{GOTerms-class}{Secondary}
\aliasA{Secondary,GOTerms-method}{GOTerms-class}{Secondary,GOTerms.Rdash.method}
\aliasA{show,GOTerms-method}{GOTerms-class}{show,GOTerms.Rdash.method}
\aliasA{Synonym}{GOTerms-class}{Synonym}
\aliasA{Synonym,GOTerms-method}{GOTerms-class}{Synonym,GOTerms.Rdash.method}
\aliasA{Term}{GOTerms-class}{Term}
\aliasA{Term,GOTerms-method}{GOTerms-class}{Term,GOTerms.Rdash.method}
\keyword{classes}{GOTerms-class}
\begin{Description}\relax
A class to represent Gene Ontology terms for a given node
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("GOTerms",
    GOId, Term, Category, Synonym, Secondary, Definition)}.
GOId, Term, and Category are required.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{GOID}:] Object of class \code{"character"} A character
stirng for the GO id of a primary node
\item[\code{Term}:] Object of class \code{"character"} A
character string that defines the role of gene product
corresponding to the primary GO id
\item[\code{Synonym}:] Object of class \code{"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.
\item[\code{Secondary}:] Object of class \code{"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
\item[\code{Definition}:] Object of class \code{"character"} Further
definition of the ontology of the primary GO id
\item[\code{Ontology}:] Object of class \code{"character"} Gene
Ontology category. Can be MF - molecular function, CC - cellular
component, or BP - biological process
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[Ontology] \code{signature(object = "GOTerms")}: The get method
for slot Ontology
\item[Ontology] \code{signature(object = "ANY")}: The get method
for slot Ontology handles missing values.
\item[Definition] \code{signature(object = "GOTerms")}: The get
method for slot Definition
\item[GOID] \code{signature(object = "GOTerms")}: The get method for
slot GOID
\item[Term] \code{signature(object = "GOTerms")}: The get method
for slot Term
\item[Secondary] \code{signature(object = "GOTerms")}: The get
method for slot Secondary
\item[Synonym] \code{signature(object = "GOTerms")}: The get method
for slot Synonym
\item[print] \code{signature(x = "GOTerms")}: The method for pretty
print
}
\end{Section}
\begin{Note}\relax
GOTerms objects are used to represent GO terms for primary GO
nodes in the annotation data package GO
\end{Note}
\begin{Author}\relax
Jianhua Zhang
\end{Author}
\begin{References}\relax
\url{http://www.geneontology.org/}
\end{References}
\begin{Examples}
\begin{ExampleCode}
  goTerms <- new("GOTerms", GOID = "GO:1234567", Term = "Test",
                 Ontology = "MF")
  GOID(goTerms)
  Term(goTerms)
  Ontology(goTerms)
\end{ExampleCode}
\end{Examples}

