\HeaderA{importGeneSets}{Import gene sets stored in GMT, GMX, GRP, and XML file formats}{importGeneSets}
\aliasA{gmtToG}{importGeneSets}{gmtToG}
\aliasA{gmxToG}{importGeneSets}{gmxToG}
\aliasA{grpToG}{importGeneSets}{grpToG}
\aliasA{xmlToG}{importGeneSets}{xmlToG}
\keyword{file}{importGeneSets}
\keyword{datagen}{importGeneSets}
\begin{Description}\relax
Imports gene sets stored in GMT, GMX, GRP, and XML file formats and
converts them to sigPathway's preferred format.
\end{Description}
\begin{Usage}
\begin{verbatim}
importGeneSets(fileNames, verbose = TRUE)
gmtToG(fileNames, verbose = TRUE)
gmxToG(fileNames, verbose = TRUE)
grpToG(fileNames, verbose = TRUE)
xmlToG(fileNames, verbose = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fileNames}] a character vector specifying the file(s) containing the gene
sets of interest
\item[\code{verbose}] a boolean to indicate whether to print debugging messages
to the R console
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
These functions read in gene sets stored in GMT, GMX, GRP, and XML
file formats and converts them to a list format that sigPathway can
use.  Redundant gene IDs in each gene set are removed during
conversion.  The \code{importGeneSets} function can read in GMT, GMX,
GRP, and XML files in one pass.  The \code{gmtToG}, \code{gmxToG},
\code{grpToG}, and \code{xmlToG} functions are specific to reading in
their respective file formats.
\end{Details}
\begin{Value}
A list containing sublists representing each imported gene set.  The
vignette contains more details about the list structure.
\end{Value}
\begin{Note}\relax
These functions do not check whether the files are in the correct
format and will give spurious output when given files in the wrong
format.  The \code{xmlToG} function requires the \code{XML} package, which
is available on CRAN.  The \code{xmlToG} function also requires XML
files to be formatted based on the MSigDB Document Type Definition.
\end{Note}
\begin{Author}\relax
Weil Lai
\end{Author}
\begin{References}\relax
\url{http://www.broad.mit.edu/cancer/software/gsea/wiki/index.php/Data_formats}
\end{References}

