\HeaderA{transitionProbability}{Compute the transition probability}{transitionProbability}
\keyword{arith}{transitionProbability}
\begin{Description}\relax
Wrapper for computing the locus-specific transition probability
\end{Description}
\begin{Usage}
\begin{verbatim}
transitionProbability(chromosome, position, TAUP = 1e+08, chromosomeAnnotation, verbose = FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{chromosome}] chromosome (integer representation)
\item[\code{position}] physical position
\item[\code{TAUP}] Scalar for computing transition probabilities (see Details).
\item[\code{chromosomeAnnotation}] Optional: chromosome annotation
\item[\code{verbose}] Logical: verbose output
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The HMM uses locus-specific transition probabilities that are calculated
as a function of the physical distance between loci. Specifically, the
probability that the locus at position \eqn{t-1}{} is not informative for
the locus at position \eqn{t}{} is calculated as \eqn{1-exp(-d/TAUP)}{},
where d is the physical distance between locus t and locus t-1.  The
default for TAUP is \eqn{1 x 10^8}{} and can be specified to acheive a
desired amount of sensitivity and specificity.  Larger values of TAUP
decreases the probability of transitioning to other states, and
therefore provides a more smooth fit.
\end{Details}
\begin{Value}
The transitionProbability function (i) transforms the physical
distance between adjacent loci to an estimate of the genomic distance
and (ii) adds an 'arm' variable to the annotation matrix.

\begin{ldescription}
\item[\code{chromosome}] chromosome 
\item[\code{position}] physical position
\item[\code{arm}] an integer.  The HMM uses the arm variable as a factor and is
fit independently to each 'arm'.
\item[\code{transitionPr}] locus-specific transition probabilities
\end{ldescription}
\end{Value}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{chromosomeAnnotation}{chromosomeAnnotation}}
\end{SeeAlso}

