\HeaderA{stamNet-class}{Classifier Net for StAM}{stamNet.Rdash.class}
\aliasA{initialize,stamNet-method}{stamNet-class}{initialize,stamNet.Rdash.method}
\aliasA{print,stamNet-method}{stamNet-class}{print,stamNet.Rdash.method}
\aliasA{writeHTML,stamNet-method}{stamNet-class}{writeHTML,stamNet.Rdash.method}
\keyword{classes}{stamNet-class}
\begin{Description}\relax
Objects of this class describe a network of classifiers as it is used by structured 
analysis of microarray data.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("stamNet", chip, root, probes)},
or by a call to \code{stam.net}.
\describe{
\item[\code{chip}] the name of the chip for which the classifier net is generated.
\item[\code{root}] the GO identifier of the node where the generation of the 
classifier net is started.
\item[\code{probes}] a character vector holding the identifiers of the probesets in 
the order as they occur in the expression matrix
}
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{chip}:] Object of class \code{"character"}, the name of the chip for 
which the classifier net is generated.
\item[\code{root}:] Object of class \code{"character"}, the GO identifier of the 
node where the generation of the       classifier net is started.
\item[\code{chippkg}:] Object of class \code{"character"}, information on the 
version of the meta data package for the chip
\item[\code{GOpkg}:] Object of class \code{"character"}, information on the version 
of the meata data package on the Gene Ontology
\item[\code{nodes}:] Object of class \code{"list"}, elements are of class 
\code{stamINode} or \code{stamLeaf}, one for each node in the classifier net.
\item[\code{leafs}:] Object of class \code{"numeric"}, indices of all leaf nodes in 
slot \code{nodes}
\item[\code{inodes}:] Object of class \code{"numeric"}, indices of all inner nodes in
slot \code{nodes}
\item[\code{probes}:] Object of class \code{"environment"}, the corresponding index 
for each probeset in the expression matrices to be analyzed
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[print] \code{signature(x = "stamNet")}: print information on the classifier
net
\item[writeHTML] \code{signature(x = "stamNet")}: generate HTML information on the 
classifier net. However, using \code{stam.writeHTML} is recommended.
}
\end{Section}
\begin{Author}\relax
Claudio Lottaz
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{stam.net}{stam.net}}, \code{\LinkA{stamLeaf-class}{stamLeaf.Rdash.class}}, 
\code{\LinkA{stamINode-class}{stamINode.Rdash.class}}
\end{SeeAlso}

