\HeaderA{copyNumber.emission}{Calculate emission probabilities for copy number}{copyNumber.emission}
\keyword{methods}{copyNumber.emission}
\begin{Description}\relax
Calculate emission probabilities for the copy number
\end{Description}
\begin{Usage}
\begin{verbatim}
copyNumber.emission(object)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] Instance of class \code{HmmOptions}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
If \code{copyNumber.ICE} = TRUE in the \code{HmmOptions} object,
then the emission probabilities for the copy number estimates take
into account the confidence scores stored in the cnConfidence slot of
the object inherting from class \code{SnpLevelSet}.  The confidence
scores are assumed to be inverse standard errors.
\end{Details}
\begin{Value}
Array of emission probabilities for the copy number estimates (on
the log scale)
\end{Value}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{copyNumber.ICE}{copyNumber.ICE}}
\end{SeeAlso}

