scaleTransitionProbability {VanillaICE} | R Documentation

## Scales the probability of transitioning between two states in the Viterbi algorithm

### Description

Scales the probability of transitioning between two states in the Viterbi algorith

### Usage

    scaleTransitionProbability(object, SCALE = 2, normalLabel = "N")

### Arguments

`object` | Object of class `HmmOptions`
`SCALE` | Numeric. See details.
`normalLabel` | Character: label used for the baseline state.

### Details

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.

### Value

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.

### Author(s)

RS

### See Also

`genomicDistance`, `transitionScale`, `HmmParameter-class`

### Examples

    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)

[Package VanillaICE version 1.2.0 Index]