\HeaderA{stamPrediction-class}{Results of Predictions by StAM}{stamPrediction.Rdash.class}
\aliasA{initialize,stamPrediction-method}{stamPrediction-class}{initialize,stamPrediction.Rdash.method}
\aliasA{print,stamPrediction-method}{stamPrediction-class}{print,stamPrediction.Rdash.method}
\aliasA{writeHTML,stamPrediction-method}{stamPrediction-class}{writeHTML,stamPrediction.Rdash.method}
\keyword{classes}{stamPrediction-class}
\begin{Description}\relax
Object of this class are returned by \code{stam.predict} and contain prediction 
results as they are computed 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("stamPrediction", fit, expr.mat, cls, testset)}, but using 
\code{stam.predict} is recommended.
\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{nodes}:] Object of class \code{"list"}, elements are of class 
\code{stamINode} or \code{stamLeaf}, one for each remaining node in the classifier 
net.
\item[\code{class.labels}:] Object of class \code{"character"}, one name for each 
class
\item[\code{best.delta}:] Object of class \code{"numeric"}, shrinkage level used for 
computing
\item[\code{cls}:] Object of class \code{"character"}, class names for 
each sample
\item[\code{probs}:] Object of class \code{"array"}, matrix of prediction 
probabilities [samples x classes x nodes]
\item[\code{predicts}:] Object of class \code{"character"}, overall prediction for 
each sample
\item[\code{testset}:] Object of class \code{"numeric"}, indeces of samples which 
belong to the test set. The other samples are assumed to be the traiing set.
\item[\code{node.results}:] Object of class \code{"list"}, performance, redundancy, 
sensitivity and specificity per node
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[image] \code{signature(x = "stamPrediction")}: molecular symptoms image, see 
\code{image.stamPrediction} for details
\item[print] \code{signature(x = "stamPrediction")}: print information on prediction
\item[writeHTML] \code{signature(x = "stamPrediction")}: generate HTML information 
on prediction, but using \code{stam.writeHTML} is recommended
}
\end{Section}
\begin{Author}\relax
Claudio Lottaz
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{stam.predict}{stam.predict}}, \code{\LinkA{image.stamPrediction}{image.stamPrediction}}, 
\code{\LinkA{stam.writeHTML}{stam.writeHTML}}
\end{SeeAlso}

