Provides functionalities for:
calculating the local score
calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution
Given a sequence of numerical score \(X_1,\dots,X_n\), the local score is defined : \(H_n = \max_{1 \leq i \leq j \leq n} \sum_{l = i}^j X_l\) This package find the value local score and the associated sub-sequence, and also sub-optimal local scores and segments. The complexity is linear with \(n\). It can be viewed as a generalization of a sliding window method, considering all windows size. In order to be pertinent, the expectation of the scores \(X_i\) should be negative. Most of the methods concerning statistical relevance implemented in this package only applied on integer scores.
Maintainer: David Robelin david.robelin@inrae.fr
Authors:
Sebastian Simon
Chris Verschelden
Charly Marty
Sabine Mercier sabine.mercier@univ-tlse2.fr
Sebastien Dejean sebastien.dejean@math.univ-toulouse.fr
Other contributors:
The authors of Eigen the library for the included version of Eigen [copyright holder]
Please refer to the vignette of this package or the manual for details on how to use this package.
An Improved Approximation For Assessing The Statistical Significance of molecular Sequence Features, Mercier and al 2003
Exact distribution for the local score of one i.i.d. random sequence, Sabine Mercier and JJ Daudin, 2001
Limit Distributions of Maximal Segmental Score among Markov-Dependent Partial Sums, Karlin and Dembo 1992
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes, Karlin and al 1990
Detection de courts segments inverses dans les genomes: methodes et applications, David Robelin 2005
A Linear Time Algorithm for Finding All Maximal Scoring Subsequences, Constable and Bates 1985