\HeaderA{test.overrepresentation}{Test statistical overrepresentation of KEGG pathways in a list of genes}{test.overrepresentation}
\keyword{file}{test.overrepresentation}
\begin{Description}\relax
Test the statistical overrepresentation of KEGG pathways in a group of genes using Fisher's exact test. The analysis can either be based on all KEGG pathways predicted by \code{\LinkA{gene2pathway}{gene2pathway}}/\code{\LinkA{gene2pathway.signaltrans}{gene2pathway.signaltrans}} or on original KEGG annotation only.
\end{Description}
\begin{Usage}
\begin{verbatim}
test.overrepresentation(genesOfInterest, predpath, KEGGonly=FALSE, cutoff=0.1, min.conf=0.9, adj.method="BY")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{genesOfInterest}] a character vector of gene identifiers (see \code{\LinkA{gene2pathway}{gene2pathway}}, \code{\LinkA{gene2pathway.signaltrans}{gene2pathway.signaltrans}}) for a gene list of interest
\item[\code{predpath}] predictions of \code{\LinkA{gene2pathway}{gene2pathway}} or \code{\LinkA{gene2pathway.signaltrans}{gene2pathway.signaltrans}}
\item[\code{KEGGonly}] use KEGG annotation only
\item[\code{cutoff}] p-value significance cutoff
\item[\code{min.conf}] filter predictions such that only those with a confidence score \textgreater{} min.conf are considered
\item[\code{adj.method}] multiple testing correction method. Default: Benjamini-Yekutieli
\end{ldescription}
\end{Arguments}
\begin{Value}
Table with two columns: KEGG pathway and adjusted p-value (adjustment according to Benjamini-Yekutieli)
\end{Value}

