\HeaderA{calls.ICE}{Indicates whether to use confidence scores of the observed copy
number estimates in the HMM}{calls.ICE}
\aliasA{calls.ICE<\Rdash}{calls.ICE}{calls.ICE<.Rdash.}
\keyword{methods}{calls.ICE}
\begin{Description}\relax
In the current framework, the confidence scores are
assumed to be the inverse of the standard error
\end{Description}
\begin{Usage}
\begin{verbatim}
calls.ICE(object)
calls.ICE(object) <- value
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] An object of class \code{HmmOptions}
\item[\code{value}] Logical.  If TRUE, confidence scores of the genotype
calls are used to calculate emission probabilities
\end{ldescription}
\end{Arguments}
\begin{Value}
Logical
\end{Value}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{SeeAlso}\relax
See the VanillaICE vignette
\end{SeeAlso}

