Class

MarkovModel

Gives a suitable representation of a Marcov Chain.

Parameters

The alphabet type | |

The type of the exploited arrays | |

The MarkovModel type |

Data Members

The MarkovModel order | |

The vector of character distribution | |

The transition matrix. |

Member Functions

Given a training set, computes the transition matrix, the character stationary distributions and the auxiliary information that give raise to an instance of MarkovModel | |

Computes the probability that a string (or a set of strings) is emitted by the MarkovModel. | |

Constructor | |

Loads an instance of MarkovModel from a file | |

Given e transition matrix, sets it as transition matrix of the MarkovModel and computes (if it is not available) the vector of character distributions and the auxiliary information | |

Stores an instance of MarkovModel on a file |

Functions

Calculates the covariance for the number of word occurrences for two words in a sequence of length n, given a background model. | |

Calculates the variance for the number of word occurrences of a word in a sequence of length n given a background model. | |

Counts kmers in a sequence. Optionally, a background model is returned. | |

Computes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel | |

Computes the variance for a set of patterns w.r.t. a set of text strings and a MarkovModel | |

Computes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel |

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