\HeaderA{genotypeEmissionCrlmm}{Estimate the emission probabilities using confidence scores from CRLMM}{genotypeEmissionCrlmm}
\keyword{htest}{genotypeEmissionCrlmm}
\begin{Description}\relax
Estimate the emission probabilities that incorporate information on
the confidence scores for the genotype calls.
\end{Description}
\begin{Usage}
\begin{verbatim}
genotypeEmissionCrlmm(genotypes, conf, pHetCalledHom = 0.001, pHetCalledHet = 0.995, pHomInNormal = 0.99, pHomInRoh = 0.999, annotation)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{genotypes}] Matrix of genotypes
\item[\code{conf}] Matirx of confidence scores (see details).
\item[\code{pHetCalledHom}] The probability that a truly heterozygous SNP is
incorrectly called homozygous (incorrect call).
\item[\code{pHetCalledHet}] The probability that a truly heterozygous SNP is
called heterozygous (correct call).
\item[\code{pHomInNormal}] The probability of a homozygous genotype call in
the 'normal' state.
\item[\code{pHomInRoh}] The probability of a homozygous genotype call in a
region of homozygosity.
\item[\code{annotation}] The cdf name (e.g., "genomewidesnp6")
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The confidence scores by crlmm are saved as an integer: 1000*log(1-p),
where p is the probability that the genotype call is correct.

The reference distribution of confidence scores are available for the following
Affymetrix platforms: affy6, nsp250, and sty250k.
\end{Details}
\begin{Value}
An R x C x X array of emission probabilities, where

R = number of loci (SNPs)
C = number of samples
S = number of states
\end{Value}
\begin{Author}\relax
R Scharpf
\end{Author}
\begin{References}\relax
RB Scharpf et al. (2008), Annals of Applied Statistics
\end{References}

