The `aneuHMM`

object is output of the function `findCNVs`

and is basically a list with various entries. The class() attribute of this list was set to "aneuHMM". For a given hmm, the entries can be accessed with the list operators 'hmm[[]]' and 'hmm$'.

`ID` |
An identifier that is used in various AneuFinder functions. |

`bins` |
A GRanges-class object containing the genomic bin coordinates, their read count and state classification. |

`segments` |
A GRanges-class object containing regions and their state classification. |

`weights` |
Weight for each component. |

`transitionProbs` |
Matrix of transition probabilities from each state (row) into each state (column). |

`transitionProbs.initial` |
Initial |

`startProbs` |
Probabilities for the first bin |

`startProbs.initial` |
Initial |

`distributions` |
Estimated parameters of the emission distributions. |

`distributions.initial` |
Distribution parameters at the beginning of the Baum-Welch. |

`convergenceInfo` |
Contains information about the convergence of the Baum-Welch algorithm. |

`convergenceInfo$eps` |
Convergence threshold for the Baum-Welch. |

`convergenceInfo$loglik` |
Final loglikelihood after the last iteration. |

`convergenceInfo$loglik.delta` |
Change in loglikelihood after the last iteration (should be smaller than |

`convergenceInfo$num.iterations` |
Number of iterations that the Baum-Welch needed to converge to the desired |

`convergenceInfo$time.sec` |
Time in seconds that the Baum-Welch needed to converge to the desired |

findCNVs

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