\HeaderA{genotypeEmission}{Emission probabilities for di-allelic genotype calls}{genotypeEmission}
\keyword{methods}{genotypeEmission}
\begin{Description}\relax
Emission probabilities for di-allelic genotype calls
\end{Description}
\begin{Usage}
\begin{verbatim}
genotypeEmission(genotypes, conf, states, probHomCall, probMissing, verbose=TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{genotypes}] matrix of integers (1=AA, 2=AB, 3=BB, 4=other)
\item[\code{conf}] Confidence estimates of the genotype calls obtained from crlmm (optional).
\item[\code{states}] character string of hidden states
\item[\code{probHomCall}] numeric: probability of a homozygous genotype call
specified in the same order as the hidden states
\item[\code{probMissing}] numeric: probability of a missing genotype call
specified in the same order as the hidden states
\item[\code{verbose}] logical
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
CRLMM provides confidences estimates of the genotype calls that can be
integrated to improve the HMM.  Because CRLMM will genotype all SNPs,
the probMissing argument is unecessary.
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{array}] Array of emission probabilities.  Dimension 1: SNPs, Dimension 2: samples, Dimension3: states
\end{ldescription}
\end{Value}

