rcpp_viterbi {srnadiff} | R Documentation

## Run the Viterbi algorithm on the HMM.

### Description

Run the Viterbi algorithm on the HMM.

### Usage

    rcpp_viterbi(chromosomeSizes, transitions, emissions, emissionThreshold, starts,
      counts, pvalues, lengths, values, minDepth, minSize, maxSize)

### Arguments

`chromosomeSizes` | the sizes of the chromosomes
`transitions` | the transition log-probabilities
`emissions` | the emission log-probabilities
`emissionThreshold` | the emission threshold
`starts` | the start log-probabilities
`counts` | the unique counts
`pvalues` | the p-values of the counts
`lengths` | the sizes of the RLEs (one list per chromosome)
`values` | the values of the RLEs (one list per chromosome)
`minDepth` | the minimum read coverage
`minSize` | the minimum size region
`maxSize` | the maximum size region

### Value

a segmentation of the chromosomes

[Package srnadiff version 1.4.0 Index]