MarkovParameters

Functions parameters global description

Functionalities for calculating the local score and calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution (S. Mercier and J.-J. Daudin (2001) <https://hal.science/hal-00714174/>) ; S. Karlin and S. Altschul (1990) <https://pmc.ncbi.nlm.nih.gov/articles/PMC53667/> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.science/hal-00937529v1/> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).

David Robelin

localScore

Package for Sequence Analysis by Local Score

Sebastian Simon

Chris Verschelden

Charly Marty

Sabine Mercier

Sebastien Dejean

The authors of Eigen the library for the included version of Eigen 

MarkovParameters function

<dl><dt>theta</dt>
<dd>alphabet used (vector of character)</dd>
<dt>lambda</dt>
<dd>transition probability matrix of size, theta x theta</dd>
<dt>score_function</dt>
<dd>vector containing the scores of each letters of the alphabet (must be in the same order as theta)</dd>
<dt>a</dt>
<dd>score strictly positive</dd>
<dt>prob0</dt>
<dd>Distribution of the first element of the Markov chain. Default to stationary distribution of lambda</dd></dl>

Arguments

Functions parameters global description — MarkovParameters

<dl>

<dt>theta</dt>
<dd>alphabet used (vector of character)</dd>


<dt>lambda</dt>
<dd>transition probability matrix of size, theta x theta</dd>


<dt>score_function</dt>
<dd>vector containing the scores of each letters of the alphabet (must be in the same order as theta)</dd>


<dt>a</dt>
<dd>score strictly positive</dd>


<dt>prob0</dt>
<dd>Distribution of the first element of the Markov chain. Default to stationary distribution of lambda</dd>

</dl>

MarkovParameters: Functions parameters global description

Description

Arguments