\HeaderA{hgTests}{A wrapper function to implement the Hypergeometric test,  
HyperGTest found withing the Category and GOstats packages.}{hgTests}
\aliasA{ppiHGTest4GO}{hgTests}{ppiHGTest4GO}
\aliasA{ppiHGTest4PFAM}{hgTests}{ppiHGTest4PFAM}
\keyword{datagen}{hgTests}
\begin{Description}\relax
This function takes the instances of the hyperGParams and conducts
a (conditional) test for over/under representation of some category
under the Hypergeometric distribution.
\end{Description}
\begin{Usage}
\begin{verbatim}
ppiHGTest4GO(parameter, filename, append=TRUE,
                      label = "Experiment name here",
                      typeGeneSet = "Describe the gene set here",
                      cs=50)

ppiHGTest4PFAM(parameter, filename, append = TRUE,
                           label = "Experiment Name Here",
                           typeGeneSet = "Describe the Gene Set Here",
                           cs = 50)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{parameter}] An object of hyperGParams.
\item[\code{filename}] A character vector. The name given to the .html file produced.
\item[\code{append}] A logical. If multiple tests are conducted using the same filename, then the 
.html file will be appended if TRUE or over-written if FALSE.
\item[\code{label}] A character. The should give a description of the experiment used to 
obtain the gene set.
\item[\code{typeGeneSet}] A character: this character vector should adequately describe the gene
set itself.
\item[\code{cs}] A numeric. This gives a cut-off for the size of the categories in which we 
conduct the test.
\end{ldescription}
\end{Arguments}
\begin{Value}
A instance of the class hyperGTest as well as an .html file.
\end{Value}
\begin{Author}\relax
T Chiang
\end{Author}

