viterbi {VanillaICE} | R Documentation |
The Viterbi algorithm for computing the most likely state sequence given a model
viterbi(beta, pi, tau, states, arm, tau.scale)
beta |
emission probabilities (log scale) |
pi |
initial state probabilities (log scale) |
tau |
transition probabilities (log scale) |
states |
character string of hidden states |
arm |
character string of chromosomal arm |
tau.scale |
scales the probability of transitioning between an altered state to a normal state relative to the probability of transitioning between two altered states. |
The Viterbi algorithm is fit independently to each chromosomal arm.
Argument tau.scale
is a matrix that scales the probability of
transitioning from an altered state to a normal state to the
probability of transitioning between two altered states.
When initializing an object of class HmmParameter
, the default
is to make the probability of transitioning from an altered state to a
normal state twice the probability of transitioning between two
altered states. Further flexibility could be obtained by replacing the
tau.scale matrix in an instance of the HmmParameter
class with
your own matrix. The dimension of this matrix must be S x S, where S
is the number of hidden states.
vector of integers
R. Scharpf