Description Usage Arguments Value Author(s) References See Also Examples

Inheritance function from `nbh`

that receives an object of GRanges class with additional column of read counts (for each strand) and call `nbh.integer`

to derive the most probable sequence of hidden states

1 2 |

`x` |
GRanges with 'values' slot used for bin counts in 1D vector of integers. |

`K` |
Number of hidden states. |

`...` |
Extra arguments passed to nbh.integer for the actual HMM computation. |

`binGR` |
GRanges of bin counts with metadata slot saved for the optimized HMM parameters including alpha, beta for the K negative binomial mixture components and TRANS (the transition probabilities) |

Yue Li

Rabiner, L. R. (1989). A tutorial on hidden Markov models and selected applications in speech recognition (Vol. 77, pp. 257-286). Presented at the Proceedings of the IEEE. doi:10.1109/5.18626

Bishop, Christopher. Pattern recognition and machine learning. Number 605-631 in Information Science and Statisitcs. Springer Science, 2006.

Capp\'e, O. (2001). H2M : A set of MATLAB/OCTAVE functions for the EM estimation of mixtures and hidden Markov models. (http://perso.telecom-paristech.fr/cappe/h2m/)

`mainSeekSingleChrom, nbh.integer`

1 | ```
if(interactive()) ?nbh # see nbh for example of nbh running on GRanges object
``` |

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