\HeaderA{getPathwayStatistics}{Give the statistics for the probe sets in a pathway}{getPathwayStatistics}
\keyword{array}{getPathwayStatistics}
\keyword{htest}{getPathwayStatistics}
\begin{Description}\relax
Gives the statistics for the probe sets associated with a pathway.
\end{Description}
\begin{Usage}
\begin{verbatim}
getPathwayStatistics(tab, phenotype, G, index, ngroups = 2,
                     statList = NULL, keepUnknownProbes = FALSE,
                     annotpkg = NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{tab}] a numeric matrix of expression values, with the rows and
columns representing probe sets and sample arrays, respectively
\item[\code{phenotype}] a numeric (or character if \code{ngroups} \textgreater{}= 2)
vector indicating the phenotype
\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{ngroups}] an integer indicating the number of groups in the expression
matrix
\item[\code{statList}] a list containing results from \code{calcTStatFast}
\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 mean, standard deviation, and 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,
mean, standard deviation, the test statistic (e.g., t-test), and the
corresponding unadjusted p-value.

If \code{ngroups} = 1, the Pearson correlation coefficient is also
returned.

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 of \code{calculate.NTk} or \code{calculate.NEk}
for example code that uses \code{getPathwayStatistics}
\end{Note}
\begin{Author}\relax
Weil Lai
\end{Author}

