\HeaderA{calculateDistance}{Calculates the physical distance between adjacent SNPs}{calculateDistance}
\aliasA{calculateDistance,SnpLevelSet-method}{calculateDistance}{calculateDistance,SnpLevelSet.Rdash.method}
\aliasA{physicalDistance}{calculateDistance}{physicalDistance}
\aliasA{physicalDistance,SnpLevelSet-method}{calculateDistance}{physicalDistance,SnpLevelSet.Rdash.method}
\keyword{methods}{calculateDistance}
\keyword{manip}{calculateDistance}
\begin{Description}\relax
Calculates the distance between adjacent SNPs.
\end{Description}
\begin{Usage}
\begin{verbatim}
calculateDistance(object)
physicalDistance(object)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] Object inheriting from \code{SnpLevelSet}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Calculates the physical distance between adjacent SNPs along a chromosome.
\end{Details}
\begin{Value}
A vector of integers
\end{Value}
\begin{Note}\relax
The transition probabilities in the Viterbi algorithm are calculated
as a function of the physical distance (d) between adjacent SNPs.

probability of staying in state S = exp(-2 * d/100*1e6)
\end{Note}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{viterbi}{viterbi}}
\end{SeeAlso}

