\HeaderA{categoryToEntrezBuilder}{Return a list mapping multi-protein complexes IDs to YEAST ids}{categoryToEntrezBuilder}
\aliasA{categoryToEntrezBuilder,CoHyperGParams-method}{categoryToEntrezBuilder}{categoryToEntrezBuilder,CoHyperGParams.Rdash.method}
\keyword{manip}{categoryToEntrezBuilder}
\begin{Description}\relax
Return a list mapping  multi-protein complexes (category) IDs to the YEAST ids annotated at
the category id.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S4 method for signature 'CoHyperGParams':
categoryToEntrezBuilder(p)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{p}] A subclass of \code{HyperGParams-class}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
End users \bold{should not} call this directly.  This method gets
called from \code{hyperGTest}.  To add support for a new
category, a new method for this generic must be defined.  Its
signature should match a subclass of
\code{HyperGParams-class} appropriate for the new
category.
\end{Details}
\begin{Value}
A list mapping category IDs to YEAST identifiers.
\end{Value}
\begin{Author}\relax
S. Falcon and N. LeMeur
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{hyperGTest}{hyperGTest}}
\code{\LinkA{CoHyperGParams-class}{CoHyperGParams.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(ScISIC)
data(essglist)
essential <- names(essglist)

params <- new("CoHyperGParams",
              geneIds=essential, 
              universeGeneIds=rownames(ScISIC),
              annotation="org.Sc.sgd.db",
              categoryName="ScISIC",
              pvalueCutoff=0.01,
              testDirection="over")

categoryToEntrezBuilder(params)[1:2]
\end{ExampleCode}
\end{Examples}

