localScore v1.0.6

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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.archives-ouvertes.fr/hal-00714174> ; S. Karlin and S. Altschul (1990) <https://www.pnas.org/content/87/6/2264> ; 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> ).

Functions in localScore

Name Description
MidSeq Protein sequence
CharSequences2ScoreSequences Convert several character sequences into score sequences
CharSequence2ScoreSequence Convert a character sequence into a score sequence
karlinMonteCarlo_double Monte Carlo - Karlin for real scores[p-value]
karlinMonteCarlo Monte Carlo - Karlin [p-value]
loadMatrixFromFile Loads matrix from csv-File
scoreSequences2probabilityVector Empirical distribution from sequences
lindley Lindley process
sequences2transmatrix Transition matrix from sequence(s)
ShortSeq Short protein sequence
stationary_distribution Stationary distribution [Markov chains]
MySeqList Several sequences
transmatrix2sequence Sampling function for Markov chains
localScore-package Package for sequence analysis by local score
loadScoreFromFile Load score from file
RealScores2IntegerScores Convert a real scores vector into an integer scores vector
scoreDictionnary2probabilityVector Check for missing scores values in the score distribution
monteCarlo_double Monte Carlo method for real score case [p-value]
localScoreC_double Local score for sequences of floating values
dico Dictionnaire
daudin Daudin [p-value] [iid]
localScoreC Local score
automatic_analysis Automatic analysis
karlin Karlin [p-value] [iid]
exact_mc Exact method for p-value [Markov chains]
mcc MCC [p-value] [iid]
monteCarlo Monte Carlo method [p-value]
LongSeq Long protein sequence
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Vignettes of localScore

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localScorePackageDocumentation.Rmd
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Details

Type Package
Date 2021-02-24
Copyright See the file COPYRIGHTS for various embedded Eigen library copyright details
License GPL (>= 2) | file LICENSE
LinkingTo Rcpp
RoxygenNote 7.1.1
LazyData true
Encoding UTF-8
SystemRequirements C++11
VignetteBuilder knitr
NeedsCompilation yes
Packaged 2021-02-24 10:24:09 UTC; drobelin
Repository CRAN
Date/Publication 2021-02-24 22:40:23 UTC

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