transitionProbability {VanillaICE} | R Documentation

## Compute the transition probability

### Description

Wrapper for computing the locus-specific transition probability

### Usage

    transitionProbability(chromosome, position, TAUP = 1e+08, chromosomeAnnotation, verbose = FALSE)

### Arguments

`chromosome` | chromosome (integer representation)
`position` | physical position
`TAUP` | Scalar for computing transition probabilities (see Details).
`chromosomeAnnotation` | Optional: chromosome annotation
`verbose` | Logical: verbose output

### Details

The HMM uses locus-specific transition probabilities that are calculated as a function of the physical distance between loci. Specifically, the probability that the locus at position t-1 is not informative for the locus at position t is calculated as 1-exp(-d/TAUP), where d is the physical distance between locus t and locus t-1. The default for TAUP is 1 x 10^8 and can be specified to acheive a desired amount of sensitivity and specificity. Larger values of TAUP decreases the probability of transitioning to other states, and therefore provides a more smooth fit.

### Value

The transitionProbability function (i) transforms the physical distance between adjacent loci to an estimate of the genomic distance and (ii) adds an 'arm' variable to the annotation matrix.

`chromosome` | chromosome
`position` | physical position
`arm` | an integer. The HMM uses the arm variable as a factor and is fit independently to each 'arm'.
`transitionPr` | locus-specific transition probabilities

### Author(s)

R. Scharpf

### See Also

`chromosomeAnnotation`

[Package VanillaICE version 1.6.0 Index]