\HeaderA{HmmOptions-class}{Class "HmmOptions"}{HmmOptions.Rdash.class}
\aliasA{annotation,HmmOptions-method}{HmmOptions-class}{annotation,HmmOptions.Rdash.method}
\aliasA{annotation<-,HmmOptions,ANY-method}{HmmOptions-class}{annotation<.Rdash.,HmmOptions,ANY.Rdash.method}
\aliasA{calculateDistance,HmmOptions-method}{HmmOptions-class}{calculateDistance,HmmOptions.Rdash.method}
\aliasA{calls.ICE,HmmOptions-method}{HmmOptions-class}{calls.ICE,HmmOptions.Rdash.method}
\aliasA{calls.ICE<-,HmmOptions,logical-method}{HmmOptions-class}{calls.ICE<.Rdash.,HmmOptions,logical.Rdash.method}
\aliasA{copyNumber.ICE,HmmOptions-method}{HmmOptions-class}{copyNumber.ICE,HmmOptions.Rdash.method}
\aliasA{copyNumber.ICE<-,HmmOptions,logical-method}{HmmOptions-class}{copyNumber.ICE<.Rdash.,HmmOptions,logical.Rdash.method}
\aliasA{copyNumber.location,HmmOptions,numeric-method}{HmmOptions-class}{copyNumber.location,HmmOptions,numeric.Rdash.method}
\aliasA{copyNumber.location,HmmOptions-method}{HmmOptions-class}{copyNumber.location,HmmOptions.Rdash.method}
\aliasA{db,HmmOptions-method}{HmmOptions-class}{db,HmmOptions.Rdash.method}
\aliasA{hmm,HmmOptions,HmmParameter-method}{HmmOptions-class}{hmm,HmmOptions,HmmParameter.Rdash.method}
\aliasA{initialize,HmmOptions-method}{HmmOptions-class}{initialize,HmmOptions.Rdash.method}
\aliasA{notes,HmmOptions-method}{HmmOptions-class}{notes,HmmOptions.Rdash.method}
\aliasA{physicalDistance,HmmOptions-method}{HmmOptions-class}{physicalDistance,HmmOptions.Rdash.method}
\aliasA{probHomCall,HmmOptions-method}{HmmOptions-class}{probHomCall,HmmOptions.Rdash.method}
\aliasA{probHomCall<-,HmmOptions,numeric-method}{HmmOptions-class}{probHomCall<.Rdash.,HmmOptions,numeric.Rdash.method}
\aliasA{show,HmmOptions-method}{HmmOptions-class}{show,HmmOptions.Rdash.method}
\aliasA{snpset,HmmOptions-method}{HmmOptions-class}{snpset,HmmOptions.Rdash.method}
\aliasA{snpset<-,HmmOptions,SnpLevelSet-method}{HmmOptions-class}{snpset<.Rdash.,HmmOptions,SnpLevelSet.Rdash.method}
\aliasA{states,HmmOptions-method}{HmmOptions-class}{states,HmmOptions.Rdash.method}
\aliasA{states<-,HmmOptions,character-method}{HmmOptions-class}{states<.Rdash.,HmmOptions,character.Rdash.method}
\aliasA{term5,HmmOptions-method}{HmmOptions-class}{term5,HmmOptions.Rdash.method}
\aliasA{term5<-,HmmOptions,numeric-method}{HmmOptions-class}{term5<.Rdash.,HmmOptions,numeric.Rdash.method}
\aliasA{[,HmmOptions-method}{HmmOptions-class}{[,HmmOptions.Rdash.method}
\keyword{classes}{HmmOptions-class}
\begin{Description}\relax
Options for fitting the hidden Markov model.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("HmmOptions", snpset, states, copyNumber.location, copyNumber.scale, copyNumber.ICE, calls.ICE, probHomCall, term5)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{states}:] Object of class \code{"character"}.  Hidden
states of the HMM.
\item[\code{snpset}:] \code{"SnpLevelSet"} instance. 
\item[\code{copyNumber.location}:] Object of class
\code{"numeric"}.  Ignored when snpset is an instance of
\code{SnpCallSet}. See \code{\LinkA{copyNumber.location}{copyNumber.location}}

\item[\code{copyNumber.scale}:] Object of class
\code{"NULLOrNumeric"}.  This slot is not currently used.  If one
has standard errors for the copy number estimates, the inverse of
the standard errors should be stored in the \code{cnConfidence}
\code{assayData} element of the snpset object.

\item[\code{copyNumber.ICE}:] Object of class \code{"logical"}. See \code{\LinkA{copyNumber.ICE}{copyNumber.ICE}}.  

\item[\code{calls.ICE}:] Object of class \code{"logical"}.  See \code{\LinkA{calls.ICE}{calls.ICE}}
\item[\code{probHomCall}:] Object of class \code{"numeric"}. The
probability of a homozygous genotype call corresponding to each of
the states. When \code{calls.ICE} is TRUE, only the first two
elements will be used.
\item[\code{term5}:] Object of class
\code{"NULLOrNumeric"}. User-specified probabilities of f(HOM |
genotype call, state).  Ignored when
\code{calls.ICE} is \code{FALSE}.  For more details, see Equation
2.7 in the manuscript that this package references.
}
\end{Section}
\begin{Section}{Methods}
\describe{

\item[[] \code{signature(x = "HmmOptions")}: 
\item[annotation] \code{signature(object = "HmmOptions")}: 
\item[annotation<-] \code{signature(object = "HmmOptions", value = "ANY")}: 
\item[calculateDistance] \code{signature(object = "HmmOptions")}: 
\item[calls.ICE] \code{signature(object = "HmmOptions")}: 
\item[calls.ICE<-] \code{signature(object = "HmmOptions", value="logical")}:     
\item[copyNumber.ICE] \code{signature(object = "HmmOptions")}: 
\item[copyNumber.ICE<-] \code{signature(object = "HmmOptions", value="logical")}:         
\item[db] \code{signature(object = "HmmOptions")}: 
\item[hmm] \code{signature(object = "HmmOptions", params = "HmmParameter")}:
\item[initialize] \code{signature(.Object = "HmmOptions")}: 
\item[notes] \code{signature(object = "HmmOptions")}: 
\item[show] \code{signature(object = "HmmOptions")}:  
\item[states] \code{signature(object = "HmmOptions")}:  
\item[states<-] \code{signature(object = "HmmOptions", value = "character")}: 
}
\end{Section}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{HmmParameter-class}{HmmParameter.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
showClass("HmmOptions")
\end{ExampleCode}
\end{Examples}

