Package for Sequence Analysis by Local Score

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Documentation for package ‘localScore’ version 2.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

Aeso	Congenital oesophageal atresia data
automatic_analysis	Automatic analysis
CharSequence2ScoreSequence	Convert a character sequence into a score sequence
CharSequences2ScoreSequences	Convert several character sequences into score sequences
daudin	Daudin [p-value] [iid]
exact_mc	Exact method for p-value [Markov chains]
HydroScore	Dictionary
karlin	Karlin [p-value] [iid]
karlinMonteCarlo	Monte Carlo - Karlin [p-value]
karlinMonteCarlo_double	Monte Carlo - Karlin [p-value]
karlin_parameters	Karlin [p-value] [iid]
lindley	Lindley process
loadMatrixFromFile	Loads matrix from csv-File
loadScoreFromFile	Load score from file
localScoreC	Local score
localScoreC_double	Local score
localScoreC_int	Local score
MarkovParameters	Functions parameters global description
maxPartialSumd	Maximum of the partial sum [probability] [iid]
mcc	MCC [p-value] [iid]
monteCarlo	Monte Carlo method [p-value]
monteCarlo_double	Monte Carlo method [p-value]
proba_theoretical_first_excursion_iid	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 sequence
proba_theoretical_ith_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 sequence
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
RealScores2IntegerScores	Convert a real scores vector into an integer scores vector
recordTimes	Calculate the record times of a sequence
scoreSequences2probabilityVector	Empirical distribution from sequences
Seq1093	Long protein sequence
Seq219	Protein sequence
Seq31	Short protein sequence
SeqListSCOPe	Several sequences
sequences2transmatrix	Transition matrix from sequence(s)
SJSyndrome	Stevens-Johnson syndrome data
stationary_distribution	Stationary distribution [Markov chains]
transmatrix2sequence	Sampling function for Markov chains