\HeaderA{rankPathways.NGSk}{Summarizes Top Pathways from One of the Pathway Analyses}{rankPathways.NGSk}
\keyword{array}{rankPathways.NGSk}
\keyword{htest}{rankPathways.NGSk}
\begin{Description}\relax
Summarizes top pathways from one of the pathway analyses (i.e.,
\code{calculate.NTk}, \code{calculate.NEk}, \code{calculate.NGSk}, or
\code{calculate.GSEA})
\end{Description}
\begin{Usage}
\begin{verbatim}
rankPathways.NGSk(res.NGSk, G, gsList, methodName = "NGSk",
                  npath = 25)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{res.NGSk}] a list from the output of \code{calculate.NGSk},
\code{calculate.NTk}, \code{calculate.NEk}, or
\code{calculate.GSEA}
\item[\code{G}] a list containing the source, title, and probe sets
associated with each curated pathway
\item[\code{gsList}] a list containing three vectors from the output of
the \code{selectGeneSets} function
\item[\code{methodName}] a character vector of length 1 giving the name of
the pathway analysis used in making \code{res.NGSk}
\item[\code{npath}] an integer indicating the number of top gene sets to
consider when ranking the top pathways
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function ranks the statistics given in \code{res.NGSk} and
summarizes the top gene sets in a tabular format similar to Table 2 in
Tian et al. (2005)
\end{Details}
\begin{Value}
A data frame showing the pathways' indices in \code{G}, gene set
category, pathway title, set size, \code{res.NGSk}'s statistics,
the corresponding q-values, and the numerical ranks for the top gene sets.
\end{Value}
\begin{Note}\relax
See the help page for \code{calculate.NGSk} for example code that
uses \code{rankPathways.NGSk}
\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}

