\HeaderA{XdeParameter-class}{Container class for storing options of the Bayesian hierarchical model}{XdeParameter.Rdash.class}
\aliasA{burnin,XdeParameter-method}{XdeParameter-class}{burnin,XdeParameter.Rdash.method}
\aliasA{burnin<-,XdeParameter,logical-method}{XdeParameter-class}{burnin<.Rdash.,XdeParameter,logical.Rdash.method}
\aliasA{directory,XdeParameter-method}{XdeParameter-class}{directory,XdeParameter.Rdash.method}
\aliasA{directory<\Rdash}{XdeParameter-class}{directory<.Rdash.}
\aliasA{directory<-,XdeParameter-method}{XdeParameter-class}{directory<.Rdash.,XdeParameter.Rdash.method}
\aliasA{firstMcmc,XdeParameter-method}{XdeParameter-class}{firstMcmc,XdeParameter.Rdash.method}
\aliasA{firstMcmc<-,XdeParameter,environment-method}{XdeParameter-class}{firstMcmc<.Rdash.,XdeParameter,environment.Rdash.method}
\aliasA{firstMcmc<-,XdeParameter,list-method}{XdeParameter-class}{firstMcmc<.Rdash.,XdeParameter,list.Rdash.method}
\aliasA{hyperparameters,XdeParameter-method}{XdeParameter-class}{hyperparameters,XdeParameter.Rdash.method}
\aliasA{hyperparameters<-,XdeParameter-method}{XdeParameter-class}{hyperparameters<.Rdash.,XdeParameter.Rdash.method}
\aliasA{initialize,XdeParameter-method}{XdeParameter-class}{initialize,XdeParameter.Rdash.method}
\aliasA{iterations,XdeParameter-method}{XdeParameter-class}{iterations,XdeParameter.Rdash.method}
\aliasA{iterations<-,XdeParameter,integer-method}{XdeParameter-class}{iterations<.Rdash.,XdeParameter,integer.Rdash.method}
\aliasA{iterations<-,XdeParameter,numeric-method}{XdeParameter-class}{iterations<.Rdash.,XdeParameter,numeric.Rdash.method}
\aliasA{output,XdeParameter-method}{XdeParameter-class}{output,XdeParameter.Rdash.method}
\aliasA{output<-,XdeParameter-method}{XdeParameter-class}{output<.Rdash.,XdeParameter.Rdash.method}
\aliasA{phenotypeLabel}{XdeParameter-class}{phenotypeLabel}
\aliasA{phenotypeLabel,XdeParameter-method}{XdeParameter-class}{phenotypeLabel,XdeParameter.Rdash.method}
\aliasA{phenotypeLabel<\Rdash}{XdeParameter-class}{phenotypeLabel<.Rdash.}
\aliasA{phenotypeLabel<-,XdeParameter,character-method}{XdeParameter-class}{phenotypeLabel<.Rdash.,XdeParameter,character.Rdash.method}
\aliasA{savedIterations}{XdeParameter-class}{savedIterations}
\aliasA{savedIterations,XdeParameter-method}{XdeParameter-class}{savedIterations,XdeParameter.Rdash.method}
\aliasA{seed,XdeParameter-method}{XdeParameter-class}{seed,XdeParameter.Rdash.method}
\aliasA{seed<-,XdeParameter,integer-method}{XdeParameter-class}{seed<.Rdash.,XdeParameter,integer.Rdash.method}
\aliasA{seed<-,XdeParameter,numeric-method}{XdeParameter-class}{seed<.Rdash.,XdeParameter,numeric.Rdash.method}
\aliasA{show,XdeParameter-method}{XdeParameter-class}{show,XdeParameter.Rdash.method}
\aliasA{showIterations}{XdeParameter-class}{showIterations}
\aliasA{showIterations,XdeParameter-method}{XdeParameter-class}{showIterations,XdeParameter.Rdash.method}
\aliasA{showIterations<\Rdash}{XdeParameter-class}{showIterations<.Rdash.}
\aliasA{showIterations<-,XdeParameter-method}{XdeParameter-class}{showIterations<.Rdash.,XdeParameter.Rdash.method}
\aliasA{studyNames}{XdeParameter-class}{studyNames}
\aliasA{studyNames,XdeParameter-method}{XdeParameter-class}{studyNames,XdeParameter.Rdash.method}
\aliasA{studyNames<\Rdash}{XdeParameter-class}{studyNames<.Rdash.}
\aliasA{studyNames<-,XdeParameter-method}{XdeParameter-class}{studyNames<.Rdash.,XdeParameter.Rdash.method}
\aliasA{thin,XdeParameter-method}{XdeParameter-class}{thin,XdeParameter.Rdash.method}
\aliasA{thin<-,XdeParameter,numeric-method}{XdeParameter-class}{thin<.Rdash.,XdeParameter,numeric.Rdash.method}
\aliasA{tuning,XdeParameter-method}{XdeParameter-class}{tuning,XdeParameter.Rdash.method}
\aliasA{tuning<-,XdeParameter-method}{XdeParameter-class}{tuning<.Rdash.,XdeParameter.Rdash.method}
\aliasA{updates,XdeParameter-method}{XdeParameter-class}{updates,XdeParameter.Rdash.method}
\aliasA{updates<-,XdeParameter-method}{XdeParameter-class}{updates<.Rdash.,XdeParameter.Rdash.method}
\keyword{classes}{XdeParameter-class}
\begin{Description}\relax
This class contains initial values for the first iteration
of the MCMC, options for saving MCMC chains, options for changing the
tuning parameters of the Metropolis-Hastings algorithm, options for
changing hyperparameters from their defaults, etc.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("XdeParameter", esetList, updates, tuning, hyperparameters, output, iterations, burnin, seed, randomSeed, genes, studies, firstMcmc, specifiedInitialValues, directory, phenotypeLabel, showIterations, verbose, studyNames)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{updates}:] Object of class \code{numeric}. The frequency
of  updates for each iteration of the chain.
\item[\code{tuning}:] Object of class \code{numeric}.  Tuning
parameters for the Metropolis-Hastings proposals 
\item[\code{hyperparameters}:] Object of class
\code{numeric}. Hyperparameters for the Bayesian hierarchical model
\item[\code{output}:] Object of class \code{numeric}. Indicator for
whether to save the MCMC chain to file.  If the value is zero, the
chain is not saved.
\item[\code{iterations}:] Object of class \code{numeric}.  The total
number of MCMC iterations.
\item[\code{burnin}:] Object of class \code{logical}.  If set to
FALSE, by default none of the chains will be saved (called for its
side-effect of setting the output to zero for each parameter).

\item[\code{notes}:] Object of class \code{character}. 
\item[\code{firstMcmc}:] Object of class \code{environment}. Values
for the first iteration of the MCMC 
\item[\code{showIterations}:] Object of class \code{logical}.
Whether to show the MCMC iteration when fitting the model
\item[\code{specifiedInitialValues}:] Object of class
\code{logical}.  If TRUE (the default), the values stored in
\code{firstMcmc} will be used for the first iteration of the MCMC. 
\item[\code{directory}:] Object of class \code{character}. Specifies
where to write the log files
\item[\code{phenotypeLabel}:] Object of class \code{character}. The
name of the binary covariate used for differential expression 
\item[\code{verbose}:] Object of class \code{logical} 
\item[\code{studyNames}:] Object of class \code{character}. Names of
the datasets
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[burnin] \code{signature(object = "XdeParameter")} logical.
See \code{\LinkA{burnin}{burnin}}
\item[burnin<-] \code{signature(object = "XdeParameter", value =
        "logical")} logical. See \code{\LinkA{burnin}{burnin}}
\item[directory] \code{signature(object = "XdeParameter")} character
string giving the path or relative path to store log files from the
MCMC chain
\item[directory<-] \code{signature(object = "XdeParameter")}Path to
store log files. 
\item[firstMcmc] \code{signature(object = "XdeParameter")} See \code{\LinkA{firstMcmc}{firstMcmc}}
\item[firstMcmc<-] \code{signature(object = "XdeParameter", value = "environment")} 
\item[firstMcmc<-] \code{signature(object = "XdeParameter", value = "list")} 
\item[hyperparameters] \code{signature(object = "XdeParameter")} See
the XdeParameterClass vignette
\item[hyperparameters<-] \code{signature(object = "XdeParameter")} See
the XdeParameterClass vignette
\item[initialize] \code{signature(.Object = "XdeParameter")} Method
for initializing an instance of the class.  The default values
provided work well in most cases.
\item[iterations] \code{signature(object = "XdeParameter")} Accessor
for the total number of MCMC iterations to run
\item[iterations<-] \code{signature(object = "XdeParameter", value =
        numeric)} The replacement method is useful for setting a
different number of iterations.
\item[iterations<-] \code{signature(object = "XdeParameter", value = "integer")} 
\item[output] \code{signature(object = "XdeParameter")} See also
\code{\LinkA{output}{output}}. This method is also defined for class \code{XdeMcmc}
\item[output<-] \code{signature(object = "XdeParameter")} See also \code{\LinkA{output}{output}} 
\item[phenotypeLabel] \code{signature(object = "XdeParameter")}
The name of a binary covariate present in each study
\item[phenotypeLabel<-] \code{signature(object = "XdeParameter", value = "character")} 
\item[savedIterations] \code{signature(object = "XdeParameter")} The
number of MCMC iterations written to file.  It is the value of the
total number of iterations divided by the thinning parameter.  See
also \code{\LinkA{output}{output}}
\item[seed] \code{signature(object = "XdeParameter")} See
\code{\LinkA{seed}{seed}}
\item[seed<-] \code{signature(object = "XdeParameter",
    value="integer")} Replacement method. See also \code{\LinkA{seed}{seed}}.    
\item[show] \code{signature(object = "XdeParameter")} Produces a
short summary of objects that are instances of the
\code{XdeParameter} class
\item[showIterations] \code{signature(object = "XdeParameter")} logical
\item[showIterations<-] \code{signature(object = "XdeParameter")} 
\item[studyNames] \code{signature(object = "XdeParameter")} Names of
the high-throughput gene expression studies
\item[studyNames<-] \code{signature(object = "XdeParameter")} 
\item[thin] \code{signature(x = "XdeParameter")} See
\code{\LinkA{output}{output}} and \code{\LinkA{thin}{thin}}
\item[thin<-] \code{signature(x = "XdeParameter", value = numeric)}
See \code{\LinkA{thin}{thin}}
\item[tuning] \code{signature(object = "XdeParameter")} See also \code{\LinkA{tuning}{tuning}}
\item[tuning<-] \code{signature(object = "XdeParameter")} 
\item[updates] \code{signature(object = "XdeParameter")} See also \code{\LinkA{updates}{updates}}
\item[updates<-] \code{signature(object = "XdeParameter")} 
}
\end{Section}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{References}\relax
R. Scharpf
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{ExpressionSetList-class}{ExpressionSetList.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
showClass("XdeParameter")
##See the XdeParameterClass vignette
\end{ExampleCode}
\end{Examples}

