\HeaderA{XdeMcmc-class}{Class for storing output from the Bayesian model}{XdeMcmc.Rdash.class}
\aliasA{\$}{XdeMcmc-class}{.Rdol.}
\aliasA{\$,XdeMcmc-method}{XdeMcmc-class}{.Rdol.,XdeMcmc.Rdash.method}
\aliasA{.standardizedDelta,XdeMcmc-method}{XdeMcmc-class}{.standardizedDelta,XdeMcmc.Rdash.method}
\aliasA{bayesianEffectSize}{XdeMcmc-class}{bayesianEffectSize}
\aliasA{bayesianEffectSize,XdeMcmc-method}{XdeMcmc-class}{bayesianEffectSize,XdeMcmc.Rdash.method}
\aliasA{bayesianEffectSize<\Rdash}{XdeMcmc-class}{bayesianEffectSize<.Rdash.}
\aliasA{bayesianEffectSize<-,XdeMcmc,matrix-method}{XdeMcmc-class}{bayesianEffectSize<.Rdash.,XdeMcmc,matrix.Rdash.method}
\aliasA{calculateBayesianEffectSize}{XdeMcmc-class}{calculateBayesianEffectSize}
\aliasA{calculateBayesianEffectSize,XdeMcmc-method}{XdeMcmc-class}{calculateBayesianEffectSize,XdeMcmc.Rdash.method}
\aliasA{calculatePosteriorAvg,XdeMcmc-method}{XdeMcmc-class}{calculatePosteriorAvg,XdeMcmc.Rdash.method}
\aliasA{directory}{XdeMcmc-class}{directory}
\aliasA{directory,XdeMcmc-method}{XdeMcmc-class}{directory,XdeMcmc.Rdash.method}
\aliasA{featureNames,XdeMcmc-method}{XdeMcmc-class}{featureNames,XdeMcmc.Rdash.method}
\aliasA{initialize,XdeMcmc-method}{XdeMcmc-class}{initialize,XdeMcmc.Rdash.method}
\aliasA{iterations,XdeMcmc-method}{XdeMcmc-class}{iterations,XdeMcmc.Rdash.method}
\aliasA{lastMcmc,XdeMcmc-method}{XdeMcmc-class}{lastMcmc,XdeMcmc.Rdash.method}
\aliasA{nrow,XdeMcmc-method}{XdeMcmc-class}{nrow,XdeMcmc.Rdash.method}
\aliasA{output,XdeMcmc-method}{XdeMcmc-class}{output,XdeMcmc.Rdash.method}
\aliasA{plot,XdeMcmc-method}{XdeMcmc-class}{plot,XdeMcmc.Rdash.method}
\aliasA{posteriorAvg,XdeMcmc-method}{XdeMcmc-class}{posteriorAvg,XdeMcmc.Rdash.method}
\aliasA{posteriorAvg<-,XdeMcmc,matrix-method}{XdeMcmc-class}{posteriorAvg<.Rdash.,XdeMcmc,matrix.Rdash.method}
\aliasA{seed,XdeMcmc-method}{XdeMcmc-class}{seed,XdeMcmc.Rdash.method}
\aliasA{show,XdeMcmc-method}{XdeMcmc-class}{show,XdeMcmc.Rdash.method}
\aliasA{studyNames,XdeMcmc-method}{XdeMcmc-class}{studyNames,XdeMcmc.Rdash.method}
\keyword{classes}{XdeMcmc-class}
\begin{Description}\relax
Stores output, including the last iteration of the MCMC.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("XdeMcmc",
  studyNames, featureNames, iterations, seed, output, directory,
  lastMcmc, posteriorAvg, bayesianEffectSize)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{studyNames}:] Object of class \code{"character"} 
\item[\code{featureNames}:] Object of class \code{"character"} 
\item[\code{iterations}:] Object of class \code{"numeric"} 
\item[\code{directory}:] Object of class \code{"character"} 
\item[\code{seed}:] Object of class \code{"integer"} 
\item[\code{output}:] Object of class \code{"numeric"} 
\item[\code{lastMcmc}:] Object of class \code{"environment"} 
\item[\code{posteriorAvg}:] Object of class \code{"NULLorMatrix"} 
\item[\code{bayesianEffectSize}:] Object of class \code{"NULLorMatrix"} 
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[\code{\$}] \code{signature(x = "XdeMcmc")} 
\item[.standardizedDelta] \code{signature(object = "XdeMcmc")}
\item[bayesianEffectSize] \code{signature(object = "XdeMcmc")} 
\item[bayesianEffectSize<-] \code{signature(object = "XdeMcmc",
        value = "matrix")} 
\item[calculatePosteriorAvg] \code{signature(object = "XdeMcmc")}:
See \code{\LinkA{calculatePosteriorAvg}{calculatePosteriorAvg}}
\item[directory] \code{signature(object = "XdeMcmc")} 
\item[featureNames] \code{signature(object = "XdeMcmc")} 
\item[initialize] \code{signature(.Object = "XdeMcmc")} 
\item[iterations] \code{signature(object = "XdeMcmc")} 
\item[lastMcmc] \code{signature(object = "XdeMcmc")} 
\item[nrow] \code{signature(x = "XdeMcmc")} 
\item[output] \code{signature(object = "XdeMcmc")} 
\item[plot] \code{signature(x = "XdeMcmc")} 
\item[posteriorAvg] \code{signature(object = "XdeMcmc")} 
\item[seed] \code{signature(object = "XdeMcmc")} 
\item[show] \code{signature(object = "XdeMcmc")} 
\item[studyNames] \code{signature(object = "XdeMcmc")} 
}
\end{Section}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{SeeAlso}\relax
The class for storing the data: \code{\LinkA{ExpressionSetList-class}{ExpressionSetList.Rdash.class}}
and the class that contains default options for fitting the Bayesian
model: \code{\LinkA{XdeParameter-class}{XdeParameter.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
##See XDE vignette:
## Not run: 
openVignette(package="XDE")
## End(Not run)
\end{ExampleCode}
\end{Examples}

