karlin

localScore

length of the sequence (at least several hundreds)

sequence_length

the probabilities for each unique score from lowest to greatest

score_probabilities

sequence_min

sequence_max

Calculates an approximated p-value of a given local score value and a long sequence length in the identically and independantly distributed model for the sequence. See also mcc() function for another approximated method in the i.i.d. model

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.archives-ouvertes.fr/hal-00714174>) ; S. Karlin and S. Altschul (1990) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC53667/> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.archives-ouvertes.fr/hal-00937529v1> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).

David Robelin

Package for Sequence Analysis by Local Score

Sebastian Simon

Sabine Mercier

Sebastien Dejean

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

karlin function

<dl><dt>localScore</dt>
<dd>the observed local score</dd>
<dt>sequence_length</dt>
<dd>length of the sequence (at least several hundreds)</dd>
<dt>score_probabilities</dt>
<dd>the probabilities for each unique score from lowest to greatest</dd>
<dt>sequence_min</dt>
<dd>minimum score</dd>
<dt>sequence_max</dt>
<dd>maximum score</dd></dl>

Arguments

Karlin [p-value] [iid] — karlin

<dl>

<dt>localScore</dt>
<dd>the observed local score</dd>


<dt>sequence_length</dt>
<dd>length of the sequence (at least several hundreds)</dd>


<dt>score_probabilities</dt>
<dd>the probabilities for each unique score from lowest to greatest</dd>


<dt>sequence_min</dt>
<dd>minimum score</dd>


<dt>sequence_max</dt>
<dd>maximum score</dd>

</dl>

karlin: Karlin [p-value] [iid]

Description

Usage

Value

Arguments

Details

Examples