\HeaderA{selectGeneSets}{Select gene sets to be analyzed in pathway analysis}{selectGeneSets}
\keyword{array}{selectGeneSets}
\keyword{htest}{selectGeneSets}
\begin{Description}\relax
Selects gene sets to be analyzed in pathway analysis based on minimum
and maximum number of probe sets to consider per pathway.
\end{Description}
\begin{Usage}
\begin{verbatim}
selectGeneSets(G, probeID, minNPS = 20, maxNPS = 500)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{G}] a list containing the source, title, and probe sets
associated with each curated pathway
\item[\code{probeID}] a character vector containing the names of probe sets
associated with a matrix of expression values
\item[\code{minNPS}] an integer specifying the minimum number of probe sets
in \code{probeID} that should be in a gene set
\item[\code{maxNPS}] an integer specifying the maximum number of probe sets
in \code{probeID} that should be in a gene set
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function selects the appropriate pathways from a large, curated
list based on the minimum and maximum number of probe sets that should
be considered in a gene set.  It creates three vectors: \code{nprobesV}
and \code{indexV} representing a sparse indicator matrix and
\code{indGused} indicating which gene sets were selected from
\code{G}.
\end{Details}
\begin{Value}
A list containing
\begin{ldescription}
\item[\code{nprobesV}] an integer vector indicating the number of probe sets
in \code{probeID} that is in each selected gene set
\item[\code{indexV}] an integer vector containing positions for each 1s in
the sparse indicator matrix
\item[\code{indGused}] an integer vector indicating which pathways in
\code{G} were chosen
\end{ldescription}
\end{Value}
\begin{Note}\relax
See the help page for \code{calculate.NTk} or \code{calculate.NEk}
for example code that uses \code{getPathwayStatistics}
\end{Note}
\begin{Author}\relax
Lu Tian, Peter Park, and Weil Lai
\end{Author}
\begin{References}\relax
Tian L., Greenberg S.A., Kong S.W., Altschuler J., Kohane I.S., Park
P.J. (2005)  Discovering statistically significant pathways in
expression profiling studies.  \emph{Proceedings of the National
Academy of Sciences of the USA}, \bold{102}, 13544-9.

\url{http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102}
\end{References}

