| scaleTransitionProbability {VanillaICE} | R Documentation |
Scales the probability of transitioning between two states in the Viterbi algorith
scaleTransitionProbability(object, SCALE = 2, normalLabel = "N")
object |
Object of class HmmOptions |
SCALE |
Numeric. See details. |
normalLabel |
Character: label used for the baseline state. |
If SCALE is 2, the probability of transitioning from an altered state back to the normal state is twice the probability of transition from an altered state to another altered state.
A matrix of dimension S x S, where S is the number of states. The
diagonal should always be 1 (we do not scale the probability of
remaining in the same state). A slot for storing this matrix is
provided in the HmmParameter class.
RS
genomicDistance, transitionScale, HmmParameter-class
data(chromosome1)
options <- new("HmmOptions",
states=c("D", "N", "L", "A"),
snpset=chromosome1,
copyNumber.location=c(1, 2, 2, 3),
probHomCall=c(0.99, 0.7, 0.99, 0.7))
scaleTransitionProbability(options)