hmm {VanillaICE} | R Documentation

## Fits hidden Markov models to high throughput SNP chip data.

### Description

Fits a hidden Markov model to high throughput SNP chip data

### Usage

    hmm(object, ...)

### Arguments

`object` | an object extending `hSet`
`...` | See details

### Details

- verbose: if TRUE, print information about the processing
- log2: if TRUE, a log2 transformation of copy number estimates is performed prior to fitting the hmm.
- arm: which arm of the chromosome to fit the hidden markov model (p, q, or both). Default is to fit to both arms.
- MISSING.CODE: missing code for genotype calls (default is NA)
- keepEmission: return emission probabilities (not recommended)
- keepLikelihod: return likelihood (not recommended)
- keepTransitionProb: return transition probabilities (not recommended)
- SCALE=1: whether to scale the transition probabilities

  ### Value

  An object of the same class

  ### Note

  further notes

  ### Author(s)

  ### References

  RB Scharpf et al. (2007), Department of Biostatistics Working Papers, Working Paper 136

  ### See Also

  The package callsConfidence is available here: http://www.biostat.jhsph.edu/~rscharpf/software/index.html

  ### Examples

      data(chromosome1)

      ## Not run:
        callsIce(hmmset) <- FALSE
        copyNumberIce(hmmset) <- FALSE
        fitVanilla <- hmm(hmmset)
        require(callsConfidence)
        callsIce(hmmset) <- TRUE
        copyNumberIce(hmmset) <- TRUE
        fitIce <- hmm(hmmset, flavor="ICE", arm="both")
      ## End(Not run)

  [Package VanillaICE version 1.0.2 Index]