\HeaderA{hgParams}{A wrapper function to build a parameter class for the 
input of the HyperGTest.}{hgParams}
\aliasA{ppiBuildParams4GO}{hgParams}{ppiBuildParams4GO}
\aliasA{ppiBuildParams4PFAM}{hgParams}{ppiBuildParams4PFAM}
\keyword{datagen}{hgParams}
\begin{Description}\relax
This function takes a gene set and conducts test for either over or under
representation of some category using the Hypergeometric distribution.

The two differences when building the parameter classes are that a conditional
test can be performed on the GO dag but not on PFAM categories and an ontology
can be assigned to GO but not to PFAM.
\end{Description}
\begin{Usage}
\begin{verbatim}
ppiBuildParams4GO(geneSet, universe, direction="over", annot="org.Sc.sgd",
                           ontology = "CC", cond=TRUE, pThresh = 0.01)
ppiBuildParams4PFAM(geneSet, universe, annot ="org.Sc.sgd",
                              direction = "over", pThresh=0.01)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{geneSet}] A character vector of genes given by the gene locus name.
\item[\code{universe}] The set of genes by which the geneSet is tested against 
for over/under representation. The genes are also given 
by the gene locus names.
\item[\code{direction}] A character. This parameter can be either set to over or under
when testing for GO categories.
\item[\code{annot}] A character. The annotation package used.
\item[\code{ontology}] A character: either CC, MF, or BP to describe the GO ontology.
\item[\code{cond}] A logical. To test within the CO dag, a conditional hypergeometric test
can be conducted.
\item[\code{pThresh}] A numeric. A p-value threshold by which the null hypothesis is rejected.
\end{ldescription}
\end{Arguments}
\begin{Value}
A object of class hyperGParams.
\end{Value}
\begin{Author}\relax
T Chiang
\end{Author}

