viterbiClonalCN {TitanCNA} | R Documentation

## Function to run the Viterbi algorithm for TitanCNA.

### Description

Function to run the Viterbi algorithm to find the optimal state path in the TitanCNA hidden Markov model (HMM). The states returned will indicate the optimal copy number and LOH state as well as the most likely clonal cluster for each data point. After running EM, use the converge parameters and the input data to infer the optimal state for each position. This function makes calls to a C subroutine that allows the algorithm to be run more efficiently.

### Usage

      viterbiClonalCN(data, convergeParams, genotypeParams = NULL)

### Arguments

`data` | `list` object that contains the components for the data to be analyzed. `chr`, `posn`, `ref`, and `tumDepth` that can be obtained using `loadAlleleCounts`, and `logR` that can be obtained using `correctReadDepth` and `getPositionOverlap` (see Example).
`convergeParams` | `list` object that is returned from the function `runEMclonalCN` in TitanCNA.
`genotypeParams` | If `convergeParams` does not contain a `genotypeParams` element, then the user can pass this as an argument.

### Details

It is difficult to interpret the output of this function directly. The user should use the function `outputTitanResults` after.

### Value

`numeric array` containing the integer states corresponding to each data point in `data`.

### Author(s)

Gavin Ha <gavinha@gmail.com>

### References

Ha, G., Roth, A., Khattra, J., Ho, J., Yap, D., Prentice, L. M., Melnyk, N., McPherson, A., Bashashati, A., Laks, E., Biele, J., Ding, J., Le, A., Rosner, J., Shumansky, K., Marra, M. A., Huntsman, D. G., McAlpine, J. N., Aparicio, S. A. J. R., and Shah, S. P. (2014). TITAN: Inference of copy number architectures in clonal cell populations from tumour whole genome sequence data. Genome Research, 24: 1881-1893. (PMID: 25060187)

### See Also

`outputTitanResults`, `loadAlleleCounts`

### Examples

    data(EMresults)

    #### COMPUTE OPTIMAL STATE PATH USING VITERBI ####
    optimalPath <- viterbiClonalCN(data, convergeParams)

[Package TitanCNA version 1.28.0 Index]