# Package for Sequence Analysis by Local Score

## 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