\HeaderA{PWAmat}{A function to compute the probe to KEGG pathway incidence matrix.}{PWAmat}
\keyword{manip}{PWAmat}
\begin{Description}\relax
For a given chip we compute the mapping from probes to KEGG pathways.
\end{Description}
\begin{Usage}
\begin{verbatim}
PWAmat(data)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{data}] The name of the chip for which the incidence matrix should
be computed.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Not much to say, just find which probes are in which pathways and
return the incidence matrix, with pathways as rows and probes as
columns. 

It would be nice to be able to specify a set of probes to use, so that 
one does not do perform the calculations using all probes if they are
not of interest.
\end{Details}
\begin{Value}
A matrix containing zero or one, depending on whether the probe
(column) is in a pathway (row).
\end{Value}
\begin{Author}\relax
R. Gentleman
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{KEGG2heatmap}{KEGG2heatmap}}, \code{\LinkA{GOmnplot}{GOmnplot}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  if(require("hgu95av2") ) {
    Am1 = PWAmat("hgu95av2")
 }
\end{ExampleCode}
\end{Examples}

