Package: localScore 2.0.1

David Robelin

localScore: Package for Sequence Analysis by Local Score

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> ).

Authors:Sebastian Simon [aut], Chris Verschelden [aut], Charly Marty [aut], David Robelin [aut, cre], Sabine Mercier [aut], Sebastien Dejean [aut], The authors of Eigen the library for the included version of Eigen [cph]

localScore_2.0.1.tar.gz
localScore_2.0.1.tar.gz(r-4.5-noble)localScore_2.0.1.tar.gz(r-4.4-noble)
localScore_2.0.1.tgz(r-4.4-emscripten)localScore_2.0.1.tgz(r-4.3-emscripten)
localScore.pdf |localScore.html✨
localScore/json (API)

# Install 'localScore' in R:
install.packages('localScore', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

2.30 score 319 downloads 28 exports 1 dependencies

Last updated 30 days agofrom:713ce12fd7. Checks:1 OK, 2 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 26 2025
R-4.5-linux-x86_64WARNINGMar 26 2025
R-4.4-linux-x86_64WARNINGMar 26 2025

Exports:automatic_analysisCharSequence2ScoreSequenceCharSequences2ScoreSequencesdaudinexact_mckarlinkarlin_parameterskarlinMonteCarlokarlinMonteCarlo_doublelindleyloadMatrixFromFileloadScoreFromFilelocalScoreClocalScoreC_doublelocalScoreC_intmaxPartialSumdmccmonteCarlomonteCarlo_doubleproba_theoretical_first_excursion_iidproba_theoretical_ith_excursion_iidproba_theoretical_ith_excursion_markovRealScores2IntegerScoresrecordTimesscoreSequences2probabilityVectorsequences2transmatrixstationary_distributiontransmatrix2sequence

Dependencies:Rcpp

Exact distribution of excursions height

Sébastien Déjean - Charly Marti - Sabine Mercier - Sebastian Simon - David Robelin

Rendered fromExcursionsheightDocumentation.Rmdusingknitr::rmarkdownon Mar 26 2025.

Last update: 2025-02-24
Started: 2025-02-24

Local Score Package

Sébastien Déjean - Sabine Mercier - Sebastian Simon - David Robelin

Rendered fromlocalScorePackageDocumentation.Rmdusingknitr::rmarkdownon Mar 26 2025.

Last update: 2025-02-24
Started: 2021-02-23

Readme and manuals

Help Manual

Help pageTopics
Congenital oesophageal atresia dataAeso
Automatic analysisautomatic_analysis
Convert a character sequence into a score sequenceCharSequence2ScoreSequence
Convert several character sequences into score sequencesCharSequences2ScoreSequences
Daudin [p-value] [iid]daudin
Exact method for p-value [Markov chains]exact_mc
DictionaryHydroScore
Karlin [p-value] [iid]karlin karlin_parameters
Monte Carlo - Karlin [p-value]karlinMonteCarlo karlinMonteCarlo_double
Lindley processlindley
Loads matrix from csv-FileloadMatrixFromFile
Load score from fileloadScoreFromFile
Local scorelocalScoreC localScoreC_double localScoreC_int
Functions parameters global descriptionMarkovParameters
Maximum of the partial sum [probability] [iid]maxPartialSumd
MCC [p-value] [iid]mcc
Monte Carlo method [p-value]monteCarlo monteCarlo_double
Probability P(Q(1)>=q a) that the height of the first excursion is greater or equal to 'a' given a i.i.d. model on the letters sequenceproba_theoretical_first_excursion_iid
Probability P(Q(i)>=q 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 sequenceproba_theoretical_ith_excursion_iid
theoretical probability of reaching the threshold score a on the i-th excursion (sequential order) of a markov's score sequenceproba_theoretical_ith_excursion_markov
Convert a real scores vector into an integer scores vectorRealScores2IntegerScores
Calculate the record times of a sequencerecordTimes
Empirical distribution from sequencesscoreSequences2probabilityVector
Long protein sequenceSeq1093
Protein sequenceSeq219
Short protein sequenceSeq31
Several sequencesSeqListSCOPe
Transition matrix from sequence(s)sequences2transmatrix
Stevens-Johnson syndrome dataSJSyndrome
Stationary distribution [Markov chains]stationary_distribution
Sampling function for Markov chainstransmatrix2sequence