\HeaderA{GOstats-defunct}{Defunct Functions in GOstats Package}{GOstats.Rdash.defunct}
\aliasA{combGOGraph}{GOstats-defunct}{combGOGraph}
\aliasA{hyperG2Affy}{GOstats-defunct}{hyperG2Affy}
\aliasA{hyperGtable}{GOstats-defunct}{hyperGtable}
\keyword{manip}{GOstats-defunct}
\begin{Description}\relax
The functions or variables listed here are no longer part of GOstats as
they are not needed (any more).
\end{Description}
\begin{Usage}
\begin{verbatim}
combGOGraph(g1, g2)
hyperGtable(probids, lib, type="MF", pvalue=0.05,
                        min.count=10, save = FALSE, output = TRUE,
                        filename = NULL, universe = NULL)
hyperG2Affy(probids, lib, type="MF", pvalue=0.05,
                         min.count=10, universe = NULL)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{g1}] A graph
\item[\code{g2}] A graph
\item[\code{probids}] A vector of Affymetrix probe IDs
\item[\code{lib}] An annotation package (e.g., \code{hgu95av2.db})
\item[\code{type}] One of "MF", "CC", "BP", indicating molecular function,
cellular component, or biological process, respectively.
\item[\code{pvalue}] The significance level used to choose GO terms
\item[\code{min.count}] The minimum number of a given GO term that must be
on the chip in order to choose that GO term. This protects against
very low p-values that result from the situation where there are
very few genes with a given GO term on the chip, but one or two are
found in the set of significant genes.
\item[\code{universe}] A character vector of unique Entrez Gene identifiers
or \code{NULL}.  This is the population (the urn) of the
Hypergeometric test.  When \code{NULL} (default), the population is
all Entrez Gene ids in the annotation package that have a GO term
annotation in the specified GO category (see \code{GOHyperG} for
more details).
\item[\code{save}] Boolean - Set to \code{TRUE} to save the resulting \code{data.frame}.
\item[\code{output}] Boolean - Set to \code{TRUE} to output the resulting
\code{data.frame} as a text file.
\item[\code{filename}] If output is set to \code{TRUE}, give the file name
for the output file.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{combGOGraph} was replaced by \code{join}.
\code{hyperGtable} was replaced by \code{summary}.
\code{hyperG2Affy} was replaced by \code{probeSetSummary}.
\end{Details}

