Package for Sequence Analysis by Local Score


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Documentation for package ‘localScore’ version 2.0.3

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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