\HeaderA{stamCV-class}{Cross Validation Information Generated by StAM}{stamCV.Rdash.class}
\aliasA{initialize,stamCV-method}{stamCV-class}{initialize,stamCV.Rdash.method}
\aliasA{print,stamCV-method}{stamCV-class}{print,stamCV.Rdash.method}
\aliasA{writeHTML,stamCV-method}{stamCV-class}{writeHTML,stamCV.Rdash.method}
\keyword{classes}{stamCV-class}
\begin{Description}\relax
Objects if this class are generated by \code{stam.cv}. It contains results of cross 
validated model fits generated in structured analysis of microarrays in order to choose
graph shrinkage levels.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form 
\code{new("stamCV", exprs, classifications, beta, chip, root)}, but it is recommended 
the use the function \code{stam.cv}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{sample.labels}:] Object of class \code{"character"}, names of samples
\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{beta}:] Object of class \code{"numeric"}, class weights, one per class
\item[\code{full.pamfit}:] Object of class \code{"nsc"}, PAM fit on all probesets
\item[\code{probs}:] Object of class \code{"array"}, matrix of cross validated 
prediction probabilities [samples x classes x nodes]
\item[\code{folds}:] Object of class \code{"list"}, buckets used in cross validation
\item[\code{results}:] Object of class \code{"data.frame"}, cross-validated root 
error rate, root performance and mean redundancy as well as remaining nodes and 
the accessible probesets for each delta
\item[\code{node.results}:] Object of class \code{"list"}, performance, redundancy, 
sensitivity and specificity per node
\item[\code{max.leafdev}:] Object of class \code{"numeric"}, performance of worst 
leaf node
\item[\code{deltas}:] Object of class \code{"numeric"}, shrinkage candidates
}
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 = "stamCV")}: print information on cross validation
\item[writeHTML] \code{signature(x = "stamCV")}: generate HTML information on cross 
validation. However, using \code{stam.writeHTML} is recommended.
}
\end{Section}
\begin{Author}\relax
Claudio Lottaz
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{stam.cv}{stam.cv}}, \code{\LinkA{stamNet-class}{stamNet.Rdash.class}}
\end{SeeAlso}

