transitionScale {VanillaICE} | R Documentation

## Scales the transition probabilities of the hidden Markov model

### Description

Accessor and replacement methods for scaling the transition probabilities

### Usage

    transitionScale(object)
    transitionScale(object) <- value

### Arguments

`object` | An object of class `HmmParameter`
`value` |

{A matrix of dimension STATES x STATES, where STATES is the number of hidden states.}

### Details

The probability of remaining in the same state, $P(S_t = S_{t+1})$ (the diagonal of the transition probability matrix) is a function of the distance between SNPs. The probability of transitioning to some other state is epsilon, where epsilon = 1 - $P(S_t = S_{t+1})$. The epsilon is split among STATES-1 states. By default, the probability of transitioning from an altered state back to the normal state is twice as likely as the probability of transitioning between two altered states. The weights for epsilon are provided in the `transitionScale` matrix in objects of class `HmmParameter`.

### Value

A matrix

### Author(s)

R. Scharpf

### See Also

`scaleTransitionProbability`

[Package VanillaICE version 1.2.0 Index]