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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