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localScore (version 2.0.1)

Package for Sequence Analysis by Local Score

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) ) ; S. Karlin and S. Altschul (1990) ; S. Mercier, D. Cellier and F. Charlot (2003) ; A. Lagnoux, S. Mercier and P. Valois (2017) ).

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Version

Install

install.packages('localScore')

Monthly Downloads

265

Version

2.0.1

License

GPL (>= 2) | file LICENSE

Maintainer

David Robelin

Last Published

February 24th, 2025

Functions in localScore (2.0.1)

Daudin [p-value] [iid]

loadScoreFromFile

Load score from file

Several sequences

Calculate the record times of a sequence

scoreSequences2probabilityVector

Empirical distribution from sequences

Exact method for p-value [Markov chains]

localScore-package

localScore: Package for Sequence Analysis by Local Score

proba_theoretical_first_excursion_iid

Probability \(P(Q(1)\geq a)\) that the height of the first excursion is greater or equal to a given a i.i.d. model on the letters sequence

Lindley process

Karlin [p-value] [iid]

Monte Carlo method [p-value]

proba_theoretical_ith_excursion_markov

theoretical probability of reaching the threshold score a on the i-th excursion (sequential order) of a markov's score sequence

proba_theoretical_ith_excursion_iid

Probability \(P(Q(i)\geq a)\) that the height of the ith excursion (sequential order) is greater or equal to a given a i.i.d. model on the letters sequence

transmatrix2sequence

Sampling function for Markov chains

Maximum of the partial sum [probability] [iid]

stationary_distribution

Stationary distribution [Markov chains]

sequences2transmatrix

Transition matrix from sequence(s)

MCC [p-value] [iid]

MarkovParameters

Functions parameters global description

CharSequences2ScoreSequences

Convert several character sequences into score sequences

Short protein sequence

CharSequence2ScoreSequence

Convert a character sequence into a score sequence

RealScores2IntegerScores

Convert a real scores vector into an integer scores vector

loadMatrixFromFile

Loads matrix from csv-File

karlinMonteCarlo

Monte Carlo - Karlin [p-value]

Long protein sequence

Congenital oesophageal atresia data

Protein sequence

Stevens-Johnson syndrome data

automatic_analysis

Automatic analysis