\HeaderA{sumSAM-class}{Class sumSAM}{sumSAM.Rdash.class}
\aliasA{print,sumSAM-method}{sumSAM-class}{print,sumSAM.Rdash.method}
\aliasA{show,sumSAM-method}{sumSAM-class}{show,sumSAM.Rdash.method}
\keyword{classes}{sumSAM-class}
\begin{Description}\relax
This class is just used for a nicer output of the summary of
an SAM-class object.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("sumSAM", ...)}
or by using the function \code{summary(object)} when object is an 
SAM-class object.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{row.sig.genes}:] Object of class \code{"numeric"} consisting
of the row numbers of the significant genes in the data matrix
\item[\code{mat.fdr}:] Object of class \code{"matrix"} containing general
information as the number of differentially expressed genes and the
estimated FDR for either one or several values of Delta.
\item[\code{mat.sig}:] Object of class \code{"data.frame"} containing gene-specific
statistics as the d-values and the q-values of the differentially expressed
genes.
\item[\code{list.args}:] Object of class \code{"list"} consisting of some of
the specified arguments of summary needed for internal use.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[print] \code{signature(x = "sumSAM")}: Prints the output of the SAM-specific
method summary.
\item[show] \code{signature(object = "sumSAM")}: Shows the output of the summary
of a SAM analysis.
}
\end{Section}
\begin{Note}\relax
SAM was developed by Tusher et al. (2001).

!!! There is a patent pending for the SAM technology at Stanford University. !!!
\end{Note}
\begin{Author}\relax
Holger Schwender, \email{holger.schw@gmx.de}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{SAM-class}{SAM.Rdash.class}}, \code{\LinkA{summary,SAM-method}{summary,SAM.Rdash.method}}
\end{SeeAlso}