\HeaderA{CoHyperGParams-class}{Class "CoHyperGParams"}{CoHyperGParams.Rdash.class}
\aliasA{annotation,HyperGParams-method}{CoHyperGParams-class}{annotation,HyperGParams.Rdash.method}
\aliasA{categoryName}{CoHyperGParams-class}{categoryName}
\aliasA{categoryName,HyperGParams-method}{CoHyperGParams-class}{categoryName,HyperGParams.Rdash.method}
\aliasA{conditional}{CoHyperGParams-class}{conditional}
\aliasA{conditional,HyperGParams-method}{CoHyperGParams-class}{conditional,HyperGParams.Rdash.method}
\aliasA{conditional<\Rdash}{CoHyperGParams-class}{conditional<.Rdash.}
\aliasA{geneIds,HyperGParams-method}{CoHyperGParams-class}{geneIds,HyperGParams.Rdash.method}
\aliasA{geneIds<\Rdash}{CoHyperGParams-class}{geneIds<.Rdash.}
\aliasA{geneIds<-,HyperGParams,logical-method}{CoHyperGParams-class}{geneIds<.Rdash.,HyperGParams,logical.Rdash.method}
\aliasA{geneIds<-,HyperGParams-method}{CoHyperGParams-class}{geneIds<.Rdash.,HyperGParams.Rdash.method}
\aliasA{HyperGParams-class}{CoHyperGParams-class}{HyperGParams.Rdash.class}
\aliasA{hyperGTest,CoHyperGParams-method}{CoHyperGParams-class}{hyperGTest,CoHyperGParams.Rdash.method}
\aliasA{isConditional}{CoHyperGParams-class}{isConditional}
\aliasA{isConditional,HyperGParams-method}{CoHyperGParams-class}{isConditional,HyperGParams.Rdash.method}
\aliasA{ontology}{CoHyperGParams-class}{ontology}
\aliasA{ontology,HyperGParams-method}{CoHyperGParams-class}{ontology,HyperGParams.Rdash.method}
\aliasA{ontology<\Rdash}{CoHyperGParams-class}{ontology<.Rdash.}
\aliasA{pvalueCutoff,HyperGParams-method}{CoHyperGParams-class}{pvalueCutoff,HyperGParams.Rdash.method}
\aliasA{pvalueCutoff<\Rdash}{CoHyperGParams-class}{pvalueCutoff<.Rdash.}
\aliasA{pvalueCutoff<-,HyperGParams-method}{CoHyperGParams-class}{pvalueCutoff<.Rdash.,HyperGParams.Rdash.method}
\aliasA{testDirection,HyperGParams-method}{CoHyperGParams-class}{testDirection,HyperGParams.Rdash.method}
\aliasA{testDirection<\Rdash}{CoHyperGParams-class}{testDirection<.Rdash.}
\aliasA{testDirection<-,HyperGParams-method}{CoHyperGParams-class}{testDirection<.Rdash.,HyperGParams.Rdash.method}
\aliasA{universeBuilder,CoHyperGParams-method}{CoHyperGParams-class}{universeBuilder,CoHyperGParams.Rdash.method}
\aliasA{universeGeneIds}{CoHyperGParams-class}{universeGeneIds}
\aliasA{universeGeneIds,HyperGParams-method}{CoHyperGParams-class}{universeGeneIds,HyperGParams.Rdash.method}
\keyword{classes}{CoHyperGParams-class}
\begin{Description}\relax
A parameter class for representing all parameters needed for running
the \code{hyperGTest} method with multiprotein complexes.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("CoHyperGParams",...)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{geneIds}:] Object of class \code{"ANY"}: A vector of
gene identifiers.  Numeric and character vectors are probably the
only things that make sense.  These are the gene ids for the
selected gene set.
\item[\code{universeGeneIds}:] Object of class \code{"ANY"}: A
vector of gene ids in the same format as \code{geneIds} defining a
subset of the gene ids on the chip that will be used as the
universe for the hypergeometric calculation.  If this is
\code{NULL} or has length zero, then all gene ids on the chip will
be used.
\item[\code{annotation}:] A string giving the name of the
annotation data package for the chip used to generate the data.
\item[\code{cateogrySubsetIds}:] Object of class \code{"ANY"}:
If the test method supports it, can be used to specify a subset of
category ids to include in the test instead of all possible
category ids.
\item[\code{categoryName}:] A string describing the category.
Usually set automatically by subclasses.  For example "ScISI".
\item[\code{pvalueCutoff}:] The p-value to use as a cutoff for
significance for testing methods that require it.  This value
will also be passed on to the result instance and used for
display and counting of significant results.  The default is
0.01.
\item[\code{testDirection}:] A string indicating whether the
test should be for overrepresentation (\code{"over"}) or
underrepresentation (\code{"under"}).
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[hyperGTest] \code{signature(p =
        "HyperGParams")}: Perform hypergeometric tests to
assess over-representation of category ids in the gene set.  See the
documentation for the generic function for details.  This method
must be called with a proper subclass of
\code{HyperGParams}.

\item[\code{geneIds(r)}, \code{geneIds(r) <- value}] Accessors for
the gene identifiers that will be used as the selected gene
list.

\item[code{annotation(object)}] Accessor for annotation

\item[\code{ontology(r)}] Accessor for GO ontology.

\item[\code{pvalueCutoff(r)}, \code{pvalueCutoff(r) <-
        value}] Accessor for the p-value cutoff.  When setting,
\code{value} should be a numeric value between zero and one.

\item[\code{testDirection}] Accessor for the test direction.  When setting,
\code{value} must be either "over" or "under".

\item[\code{universeGeneIds(r)}] accessor for vector of gene
identifiers.

\item[\code{isConditional(r)}] Returns \code{TRUE} if the instance
has its conditional flag set


}
\end{Section}
\begin{Author}\relax
S. Falcon and N. LeMeur
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{HyperGResult-class}{HyperGResult.Rdash.class}}
\code{\LinkA{CoHyperGResult-class}{CoHyperGResult.Rdash.class}}
\code{\LinkA{hyperGTest}{hyperGTest}}
\end{SeeAlso}

