\HeaderA{writeSigPathway}{Write results of pathway analysis to HTML format}{writeSigPathway}
\aliasA{writeSP}{writeSigPathway}{writeSP}
\keyword{array}{writeSigPathway}
\keyword{htest}{writeSigPathway}
\begin{Description}\relax
Writes the table of top-ranked pathways and their associated probe set
to HTML files.
\end{Description}
\begin{Usage}
\begin{verbatim}
writeSigPathway(spList, resDir = getwd(),
                outputDirName = "sigPathway_results",
                topIndexFileName = "TopPathwaysTable.html")
writeSP(rpDF, gpsList, parameterList = NULL, resDir = getwd(),
        outputDirName = "sigPathway_results",
        topIndexFileName = "TopPathwaysTable.html")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{spList}] a list containing the output from the
\code{runSigPathway} function
\item[\code{rpDF}] a data frame of top-ranked pathways from
\code{rankPathways} or \code{rankPathways.NGSk}
\item[\code{gpsList}] a list containing data frames of probes represented in
gene sets from \code{getPathwayStatistics} or
\code{getPathwayStatistics.NGSk}
\item[\code{parameterList}] a list containing the values of parameters used
in the analysis
\item[\code{resDir}] a character string specifying the file directory to
write the results
\item[\code{outputDirName}] a character string specifying the folder to write
the results within \code{resDir}
\item[\code{topIndexFileName}] a character string specifying the name for the
HTML file containing the table of top-ranked pathways
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
These functions export the results of the pathway analysis (e.g.,
\code{runSigPathway}) to several HTML files.  The user can then
quickly browse through the files for genes of interest within the
top-ranked genes.
\end{Details}
\begin{Value}
None returned
\end{Value}
\begin{Note}\relax
This function only uses the output of \code{runSigPathway} to
generate the HTML files.  Please see the help page of
\code{runSigPathway} for example usage.  The \code{writeSP} function
should be used for those who have taken calculated the pathway
statistics separately as shown in the help file of \code{calculate.NTk},
\code{calculate.NEk}, and \code{calculate.NGSk}
\end{Note}
\begin{Author}\relax
Weil Lai
\end{Author}

