\HeaderA{copynumberEmission}{Emission probabilities for copy number}{copynumberEmission}
\keyword{methods}{copynumberEmission}
\begin{Description}\relax
Emission probabilities for copy number
\end{Description}
\begin{Usage}
\begin{verbatim}
copynumberEmission(copynumber, states, mu, uncertainty, takeLog, verbose = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{copynumber}] class matrix
\item[\code{states}] class character
\item[\code{mu}] class numeric: mean of hidden states for Gaussian
\item[\code{uncertainty}] uncertainty of copy number estimates
\item[\code{takeLog}] whether to take the log of the copy number AND the mu argument
\item[\code{verbose}] logical
\end{ldescription}
\end{Arguments}
\begin{Value}
\begin{ldescription}
\item[\code{array}] Array of emission probabilities.  Dimension 1: SNPs, Dimension 2: samples, Dimension3: states
\end{ldescription}
\end{Value}

