\HeaderA{genomicDistance}{A rough estimate of the genomic distance between SNPs}{genomicDistance}
\aliasA{genomicDistance<\Rdash}{genomicDistance}{genomicDistance<.Rdash.}
\aliasA{tau}{genomicDistance}{tau}
\keyword{methods}{genomicDistance}
\begin{Description}\relax
Calculates the genomic distance between SNPs as a function of the
physical distance.  This distance is used for calculating transition
probabilities in the viterbi algorithm.
\end{Description}
\begin{Usage}
\begin{verbatim}
genomicDistance(object)
tau(object)
genomicDistance(object) <- value
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] An object inheriting from \code{HmmOptions}
\item[\code{value}] A vector of length T - 1, where T is the number of SNPs
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The genomic distance is calculated as exp(-2*d), where d is the
physical distance in 100MB units.

In the Viterbi algorithm, the probability of remaining in state S at
SNP t+1 is the genomic distance.  The probability of transitioning to
one of the alternative states is 1 - the genomic distance.  The
\code{transitionScale} function can be used to give more weight to
transitioning back to the baseline ('normal') state.
\end{Details}
\begin{Value}
A numeric vector with length T-1.
\end{Value}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{transitionScale}{transitionScale}}
\end{SeeAlso}

