Description Usage Arguments References

View source: R/methods-PennParam.R

Parameters for the PennCNV Hidden Markov model

1 2 3 4 5 6 7 8 9 10 11 12 |

`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 |

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

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