\HeaderA{GOHyperGResult-class}{Class "GOHyperGResult"}{GOHyperGResult.Rdash.class}
\aliasA{condGeneIdUniverse,GOHyperGResult-method}{GOHyperGResult-class}{condGeneIdUniverse,GOHyperGResult.Rdash.method}
\aliasA{conditional,GOHyperGResult-method}{GOHyperGResult-class}{conditional,GOHyperGResult.Rdash.method}
\aliasA{expectedCounts,GOHyperGResult-method}{GOHyperGResult-class}{expectedCounts,GOHyperGResult.Rdash.method}
\aliasA{geneCounts,GOHyperGResult-method}{GOHyperGResult-class}{geneCounts,GOHyperGResult.Rdash.method}
\aliasA{geneIdUniverse,GOHyperGResult-method}{GOHyperGResult-class}{geneIdUniverse,GOHyperGResult.Rdash.method}
\aliasA{goDag}{GOHyperGResult-class}{goDag}
\aliasA{goDag,GOHyperGResult-method}{GOHyperGResult-class}{goDag,GOHyperGResult.Rdash.method}
\aliasA{htmlReport,GOHyperGResult-method}{GOHyperGResult-class}{htmlReport,GOHyperGResult.Rdash.method}
\aliasA{isConditional,GOHyperGResult-method}{GOHyperGResult-class}{isConditional,GOHyperGResult.Rdash.method}
\aliasA{oddsRatios,GOHyperGResult-method}{GOHyperGResult-class}{oddsRatios,GOHyperGResult.Rdash.method}
\aliasA{pvalues,GOHyperGResult-method}{GOHyperGResult-class}{pvalues,GOHyperGResult.Rdash.method}
\aliasA{selectedGenes}{GOHyperGResult-class}{selectedGenes}
\aliasA{summary,GOHyperGResult-method}{GOHyperGResult-class}{summary,GOHyperGResult.Rdash.method}
\keyword{classes}{GOHyperGResult-class}
\begin{Description}\relax
This class represents the results of a test for overrepresentation
of GO categories among genes in a selected gene set based upon the
Hypergeometric distribution.

For details on extracting information from this object, be sure to
read the accessor documentation in the Category package:
\LinkA{HyperGResult-accessors}{HyperGResult.Rdash.accessors}.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("GOHyperGResult", ...)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{goDag}:] Object of class \code{"graph"} representing
the DAG of GO terms tested.
\item[\code{pvalue.order}:] Object of class \code{"integer"}.
The sort order of the computed p-values.
\item[\code{annotation}:] Object of class \code{"character"}.  The
name of the annotation data package used in the analysis.
\item[\code{geneIds}:] Object of class \code{"ANY"}.  The
intersection of the gene identifiers given as input and the
computed gene universe.
\item[\code{testName}:] Object of class \code{"character"}.
Identifies the testing method used to produce this result instance.
\item[\code{pvalueCutoff}:] Object of class \code{"numeric"}.
The cutoff for significance used for some testing methods.
Also used for pretty display in the \code{show} method.

}
\end{Section}
\begin{Section}{Extends}
Class \code{"HyperGResultBase"}, directly.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[goDag] \code{signature(r = "GOHyperGResult")}:
return the \code{graph} instance representing the DAG of the
GO terms that were tested.

\item[condGeneIdUniverse] \code{signature(r =
        "GOHyperGResult")}: return a list named by the
tested GO terms.  Each element of the list is a vector of the
remaining gene identifiers (from the gene universe) annotated at
the corresponding GO term after the identifiers from significant
children were removed.  This is only available when the
calculation performed used the conditional Hypergeometric
algorithm.

\item[summary] \code{signature(r = "GOHyperGResult")}: Returns a
\code{data.frame} summarizing the test result.  Optional
arguments \code{pvalue} and \code{categorySize} allow
specification of maximum p-value and minimum categorySize,
respectively.  Optional argument \code{htmlLinks} is a logical
value indicating whether to add HTML links (useful in
conjunction with xtables print method with \code{type} set to
\code{"html"}).

\item[htmlReport] \code{signature(r = "GOHyperGResult")}: Write an
HTML version of the table produced by the \code{summary} method.
The path of a file to write the report to can be specified using
the \code{file} argument.  The default is \code{file=""} which
will cause the report to be printed to the screen.  If you wish
to create a single report comprising multiple results you can
set \code{append=TRUE}.  The default is \code{FALSE} (overwrite
preexisting report file).  You can specify a string to use as an
identifier for each table by providing a value for the
\code{label} argument.  Additional named arguments will be
passed to the \code{summary} method.

\item[description] \code{signature(object = "GOHyperGResult")}:
Return a string giving a one-line description of the result.

}
\end{Section}
\begin{Author}\relax
Seth Falcon
\end{Author}
\begin{SeeAlso}\relax
\LinkA{HyperGResult-accessors}{HyperGResult.Rdash.accessors}
\end{SeeAlso}

