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]