Package: localScore 2.0.5

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 (D. Robelin, S. Déjean, S. Mercier (2025) <doi:10.24072/pcjournal.650> ; 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_2.0.5.tar.gz
localScore_2.0.5.tar.gz(r-4.7-arm64)localScore_2.0.5.tar.gz(r-4.7-x86_64)localScore_2.0.5.tar.gz(r-4.6-arm64)localScore_2.0.5.tar.gz(r-4.6-x86_64)
localScore_2.0.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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

2.45 score 14 scripts 541 downloads 28 exports 1 dependencies

Last updated from:8f014d9830. Checks:4 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING156
linux-devel-x86_64WARNING172
source / vignettesOK249
linux-release-arm64WARNING152
linux-release-x86_64WARNING162
wasm-releaseOK125

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
Introduction | Computation method | Definition of a mathematical excursion | Toy examples | A study case | Optimal excursion, the local score | Sub optimal excursions | With a reverse lecture of the protein | What about the excursion realising the local score
Rendered fromExcursionsheightDocumentation.Rmdusingknitr::rmarkdown

Last update: 2026-04-21
Started: 2025-02-24

Local Score Package
Citation | Introduction | In brief | Case of I.I.D. integer score sequence | Generating an I.I.D. score sequence for this example | Graphical representation via the Lindley process | Finding the maximal sum subsequence and all strictly positive sum subsequences | Calculating p-value of local score | Case of markov integer score sequence | Generating a markov score sequence for this example | Case of various dependent structure sequence via Monte-Carlo approach | Generating a complex dependent structure score sequence for this example | Calculating p-value of local score by Monte Carlo simulation | Case of $i$th excursion (sequential order) | Calculating $p$-value of $i$th excursion | Local Score computation methods | A first example: function ``localScoreC()'' | Example with real scores | Example of alphabetical sequence associated to a scoring function | $p$-Value computation methods | Simulating computation: functions "monteCarlo()" | A mixed method: functions "karlinMonteCarlo()" | Exact method for integer scores: function ``daudin()'' | How to use the exact method for real scores | Approximate method of Karlin et al.: function ``karlin()'' | An improved approximate method: function ``mcc()'' | An automatic method: function ``automatic_analysis()'' | Markovian model of the sequence : function exact_mc() | Other Functions | Lindley Process: to visualize optimal and suboptimal segments | Record times: gives the record times of a sequence | Score Loading Function | Empirical distribution: function "scoreSequences2probabilityVector()" | Case study | Medium sequence | Local score computation and parameter model setings | Parameter model setings | Exact method | Approximated method | Improved approximation | Monte Carlo | Result and time computation comparison | Short sequence | Results | Large sequence | Several sequences | A larger example with a SCOP data base | File Formats | Sequence Files | Score Files | Transition Matrix Files
Rendered fromlocalScorePackageDocumentation.Rmdusingknitr::rmarkdown

Last update: 2026-04-21
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