\HeaderA{stamFit-class}{Model Fit Generated by StAM}{stamFit.Rdash.class}
\aliasA{initialize,stamFit-method}{stamFit-class}{initialize,stamFit.Rdash.method}
\aliasA{print,stamFit-method}{stamFit-class}{print,stamFit.Rdash.method}
\aliasA{writeHTML,stamFit-method}{stamFit-class}{writeHTML,stamFit.Rdash.method}
\keyword{classes}{stamFit-class}
\begin{Description}\relax
Objects of this class hold a model fit as it is generated by structured analysis of 
microarray data. The function \code{stam.fit} returns such objects. They are handed on 
to \code{stam.predict} for predictions.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form 
\code{new("stamFit", cv, exprs, alpha, delta, max.nodes, collapse.scnodes)}, but it is 
recommended to use the function \code{stam.fit}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{sample.classes}:] Object of class \code{"character"}, class names for 
each sample
\item[\code{class.labels}:] Object of class \code{"character"}, one name for each 
class
\item[\code{prior}:] Object of class \code{"numeric"}, prior class probabilities 
according to prevalence
\item[\code{full.pamfit}:] Object of class \code{"nsc"}, PAM fit on all probesets
\item[\code{alpha}:] Object of class \code{"numeric"}, performance vs. redundancy 
weight(s)
\item[\code{beta}:] Object of class \code{"numeric"}, class weights, one per class
\item[\code{delta}:] Object of class \code{"numeric"}, shrinkage level given by the 
user
\item[\code{best.delta}:] Object of class \code{"numeric"}, shrinkage level used for 
computing
\item[\code{default.delta}:] Object of class \code{"numeric"}, default shrinkage 
level suggested by \code{stam.fit}
\item[\code{scores}:] Object of class \code{"matrix"}, compound scores weighted 
using the provided alpha(s)
\item[\code{alpha.tab}:] Object of class \code{"matrix"}, results comparing alphas
\item[\code{node.results}:] Object of class \code{"list"}, performance, redundancy, 
sensitivity and specificity per node
\item[\code{collapse.scnodes}:] Object of class \code{"logical"}, whether single 
children nodes are removed after shrinkage
}
See \code{stamNet-class} for slots \code{chip}, \code{root}, \code{chippkg}, 
\code{GOpkg}, \code{nodes}, \code{leafs}, \code{inodes} and \code{probes}.
\end{Section}
\begin{Section}{Extends}
Class \code{"stamNet"}, directly.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[print] \code{signature(x = "stamFit")}: print information on the model fit.
\item[writeHTML] \code{signature(x = "stamFit")}: generate HTML information on the 
model fit, but using \code{stam.writeHTML} is recommended.
}
\end{Section}
\begin{Author}\relax
Claudio Lottaz
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{stam.fit}{stam.fit}}, \code{\LinkA{stamNet-class}{stamNet.Rdash.class}}
\end{SeeAlso}

