\HeaderA{hyperGtable}{Table from GOHyperG}{hyperGtable}
\keyword{manip}{hyperGtable}
\keyword{htest}{hyperGtable}
\begin{Description}\relax
Output a table from a call to \code{\LinkA{GOHyperG}{GOHyperG}}.
\end{Description}
\begin{Usage}
\begin{verbatim}
hyperGtable(probids, lib, type = "MF", pvalue = 0.05, min.count = 10,
save = FALSE, output = TRUE, filename = NULL, universe = NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{probids}] A vector of Affymetrix probe IDs
\item[\code{lib}] An annotation package (e.g., \code{hgu95av2})
\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{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.
\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).
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function will take a vector of Affymetrix IDs and output a
\code{data.frame} containing information on all GO terms that are found
significant in a call to \code{\LinkA{GOHyperG}{GOHyperG}}.
\end{Details}
\begin{Value}
A \code{data.frame} containing the following columns:

GO Term - The GOID associated with a given GO term

Description - The description for that GO term

p-values - The p-value associated with that GO term

Number significant - The number of genes in the vector of Affymetrix IDs
with that particular GO term

Number on chip - The number of genes on the Affymetrix chip with that
particular GO term.
\end{Value}
\begin{Author}\relax
James W. MacDonald <jmacdon@med.umich.edu>
\end{Author}
\begin{Examples}
\begin{ExampleCode}
library("hgu95av2")
probids <- ls(hgu95av2GENENAME)[1:10]
hyperGtable(probids, "hgu95av2", save = TRUE, output = FALSE)
\end{ExampleCode}
\end{Examples}

