viterbi {VanillaICE} | R Documentation |
The Viterbi algorithm for computing the most likely state sequence given a model
viterbi(initialStateProbs, emission, tau, arm, tau.scale, verbose = FALSE, chromosome, position, sampleNames, locusNames, normalIndex, returnLikelihood = FALSE)
initialStateProbs |
initial state probabilities (log scale) |
emission |
matrix of log emission probabilities (one sample is a matrix) |
tau |
transition probabilities (original scale) |
arm |
numeric or character string indicating chromosomal arm |
tau.scale |
matrix to scale the probability of transitioning between states. |
verbose |
Logical |
chromosome |
chromosome |
position |
physical position |
sampleNames |
sample labels |
locusNames |
labels for loci |
normalIndex |
index corresponding to the normal state. See details |
returnLikelihood |
whether to return the 'loglikelihood' |
The Viterbi algorithm is fit independently to each chromosomal arm if arm is specified.
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. If missing,
tau.scale is 1 (no scaling)
matrix |
predicted states |
R. Scharpf