Description Usage Arguments See Also

This function is a workhorse of `find.hmm.states`

. It
operates on the individual chromosomes/samples and is not called
directly by users.

1 2 3 4 | ```
states.hmm.func(sample, chrom, dat, datainfo = clones.info, vr = 0.01,
maxiter = 100, aic = FALSE, bic = TRUE, delta = 1,
nlists = 1, eps = .01, print.info = FALSE,
diag.prob = .99)
``` |

`sample` |
sample identifier |

`chrom` |
chromosome identifier |

`dat` |
dataframe with clones in the rows and samples in the columns |

`datainfo` |
dataframe containing the clones information that is used to map each clone of the array to a position on the genome. Has to contain columns with names Clone/Chrom/kb containing clone names, chromosomal assignment and kb positions respectively |

`vr` |
Initial experimental variance |

`maxiter` |
Maximum number of iterations |

`aic` |
TRUE or FALSE variable indicating whether or nor AIC criterion should be used for model selection (see DETAILS) |

`bic` |
TRUE or FALSE variable indicating whether or nor BIC criterion should be used for model selection (see DETAILS) |

`delta` |
numeric vector of penalty factors to use with BIC criterion. If BIC is true, delta=1 is always calculated (see DETAILS) |

`nlists` |
defaults to 1 when aic=TRUE, otherwise > 1 |

`eps` |
parameter controlling the convergence of the EM algorithm. |

`print.info` |
print.info = T allows diagnostic information to be printed on the screen. |

`diag.prob` |
parameter controlling the construction of the initial transition probability matrix. |

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