\HeaderA{writeGmt}{writeGmt}{writeGmt}
\keyword{data}{writeGmt}
\begin{Description}\relax
This function writes out SMC objects into .gmt file format
\end{Description}
\begin{Usage}
\begin{verbatim}
writeGmt(fname, cl)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fname}] name of the file to be written out 
\item[\code{cl}] list of SMC objects 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The .gmt file format is a tab delimited file format used to store gene lists. These gene lists are stored row by row. The first column is the gene set name. The second column is a brief description, and every entry after that is a gene within that gene set.
\end{Details}
\begin{Author}\relax
Kyle Furge \textless{}kyle.furge@vai.org\textgreater{} and Karl Dykema \textless{}karl.dykema@vai.org\textgreater{}
\end{Author}
\begin{References}\relax
\url{http://www.broad.mit.edu/gsea/doc/data_formats.html#gmt }
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{readGmt}{readGmt}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

        datadir <- system.file("data", package = "PGSEA")
        sample <- readGmt(file.path(datadir, "sample.gmt"))
        str(sample)

## Not run: 
        writeGmt(paste(datadir,"/output.gmt",sep=""),sample)
## End(Not run)

\end{ExampleCode}
\end{Examples}

