\HeaderA{copyNumber.ICE}{Indicates whether to use confidence scores of the observed copy
number estimates in the HMM}{copyNumber.ICE}
\aliasA{copyNumber.ICE<\Rdash}{copyNumber.ICE}{copyNumber.ICE<.Rdash.}
\keyword{methods}{copyNumber.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}
copyNumber.ICE(object)
copyNumber.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 copy number
estimates are used to calculate emission probabilities.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
If TRUE, the confidence scores (assumed to be inverse standard
errors) are used by the hidden Markov model.  This has the
desirable consequence of providing more local smmoothing for
precise estimates of copy number and more global smoothing for
copy number estimates with higher standard errors. When FALSE, a
robust estimate of the chip variability is calculated across all
of the autosomes.
\end{Details}
\begin{Value}
Logical
\end{Value}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{SeeAlso}\relax
See the VanillaICE vignette
\end{SeeAlso}

