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localScore (version 1.0.11)

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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Install

install.packages('localScore')

Monthly Downloads

420

Version

1.0.11

License

GPL (>= 2) | file LICENSE

Maintainer

David Robelin

Last Published

November 2nd, 2023

Functions in localScore (1.0.11)

SJSyndrome.data

Stevens-Johnson syndrome data
RealScores2IntegerScores

Convert a real scores vector into an integer scores vector
exact_mc

Exact method for p-value [Markov chains]
aeso.data

Deprecated. Use 'Aeso' instead.
MidSeq

Deprecated. Use 'Seq219' instead.
CharSequences2ScoreSequences

Convert several character sequences into score sequences
automatic_analysis

Automatic analysis
HydroScore

Dictionnaire
SeqListSCOPe

Several sequences
karlin

Karlin [p-value] [iid]
Seq1093

Long protein sequence
localScoreC

Local score
ShortSeq

Deprecated. Use 'Seq31' instead.
loadMatrixFromFile

Loads matrix from csv-File
lindley

Lindley process
karlinMonteCarlo

Monte Carlo - Karlin [p-value]
Seq219

Protein sequence
karlinMonteCarlo_double

Monte Carlo - Karlin for real scores[p-value]
scoreDictionnary2probabilityVector

Check for missing scores values in the score distribution
Seq31

Short protein sequence
maxPartialSumd

Maximum of the partial sum [probability] [iid]
mcc

MCC [p-value] [iid]
sequences2transmatrix

Transition matrix from sequence(s)
scoreSequences2probabilityVector

Empirical distribution from sequences
localScoreC_double

Local score for sequences of floating values
stationary_distribution

Stationary distribution [Markov chains]
daudin

Daudin [p-value] [iid]
monteCarlo

Monte Carlo method [p-value]
dico

Deprecated. Use 'HydroScore' instead.
monteCarlo_double

Monte Carlo method for real score case [p-value]
loadScoreFromFile

Load score from file
localScore-package

Package for sequence analysis by local score
transmatrix2sequence

Sampling function for Markov chains
LongSeq

Deprecated. Use 'Seq1093' instead.
MySeqList

Deprecated. Use 'SeqListSCOPe' instead.
CharSequence2ScoreSequence

Convert a character sequence into a score sequence
Aeso

Congenital oesophageal atresia data