PennParam {MinimumDistance} | R Documentation

## Constructor for class `PennParam`

### Description

Parameters for the PennCNV Hidden Markov model

### Usage

    PennParam(
      states,
      referenceState = "222",
      prLessLikelyCN = 9e-04,
      prNonMendelian = 1.5e-06,
      prInitialStateNotDiploid = 4/5,
      prTransitionToNewState = 0.5,
      tauNM = 0.01
    )

    ## S4 method for signature 'PennParam'
    show(object)

### Arguments

`states` | character vector of possible trio states
`referenceState` | the reference (normal) trio copy number state (typically '222')
`prLessLikelyCN` | as defined in Wang et al. 2007, this is the probability of the less likely allele-specific copy numbers for the trio
`prNonMendelian` | the prior probability of a non-Mendelian copy number alteration
`prInitialStateNotDiploid` | initial probability for non-diploid states
`prTransitionToNewState` | probability of transitioning to a new state
`tauNM` | probability of transitioning from a Mendelian given previous event was non-Mendelian (and vice versa).
`object` | a `PennParam` object

### References

Wang et al., Genome Res. 2007 Nov;17(11):1665-74. PMID: 17921354

[Package MinimumDistance version 1.31.1 Index]