\HeaderA{getPathwayStatistics.NGSk}{Give the statistics for the probe sets in a pathway}{getPathwayStatistics.NGSk}
\keyword{array}{getPathwayStatistics.NGSk}
\keyword{htest}{getPathwayStatistics.NGSk}
\begin{Description}\relax
Gives the statistics for the probe sets associated with a pathway.
\end{Description}
\begin{Usage}
\begin{verbatim}
getPathwayStatistics.NGSk(statV, probeID, G, index,
                          keepUnknownProbes = FALSE, annotpkg = NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{statV}] a numeric vector of test statistic (not p-values) for
each individual probe/gene
\item[\code{probeID}] a character vector containing the names of probe sets
associated with a matrix of expression values
\item[\code{G}] a list containing the source, title, and probe sets
associated with each curated pathway
\item[\code{index}] an integer vector specifying the pathway(s) to summarize
in \code{G}
\item[\code{keepUnknownProbes}] a boolean indicating whether to keep the
names of probe sets not represented in tab in the summary data
frame
\item[\code{annotpkg}] a character vector specifying the name of the
BioConductor annotation package to use to fetch accession numbers,
Entrez Gene IDs, gene name, and gene symbols
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function gives the test statistic for each probe in the pathway
as indicated in \code{G[[index]]}.
\end{Details}
\begin{Value}
A list containing data frames (1 per pathway) with the probes' name
and the corresponding test statistic.

If a valid \code{annotpkg} is specified, the probes' accession
numbers, Entrez Gene IDs, gene name, and gene symbols are also
returned.  This option only works if the probes in the gene set list
\code{G} are manufacturer IDs corresponding to those used in making
the BioConductor annotation package.
\end{Value}
\begin{Note}\relax
See the help page for \code{calculate.NGSk} for example code that
uses \code{getPathwayStatistics.NGSk}
\end{Note}
\begin{Author}\relax
Weil Lai
\end{Author}

