\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, sds, takeLog, verbose = TRUE,
na.rm=TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{copynumber}] matrix
\item[\code{states}] character string
\item[\code{mu}] numeric: mean of hidden states for Gaussian
\item[\code{sds}] standard deviations of copy number estimates
\item[\code{takeLog}] logical: if TRUE, this function takes the log of the
copy number AND mu arguments to this function
\item[\code{verbose}] logical
\item[\code{na.rm}] The default is to ignore missing values when calculating robust standard deviations
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
By default, this func estimates the scale parameter for the Normal
distribution from the supplied data using the median absolute
deviation (MAD). However, different standard deviations can be
supplied by the user with the argument \code{sds}. The supplied
standard deviations must be of the same dimension as the copy number
matrix.
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{array}] Array of emission probabilities on the log scale.
Dimension 1: SNPs, Dimension 2: samples, Dimension3: states
\end{ldescription}
\end{Value}
\begin{SeeAlso}\relax
\code{\LinkA{genotypeEmission}{genotypeEmission}}, \code{\LinkA{genotypeEmissionCrlmm}{genotypeEmissionCrlmm}}
\end{SeeAlso}

