Package for Sequence Analysis by Local Score

---

Documentation for package ‘localScore’ version 1.0.11

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

Help Pages

localScore-package	Package for sequence analysis by local score
Aeso	Congenital oesophageal atresia data
aeso.data	Deprecated. Use 'Aeso' instead.
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]
dico	Deprecated. Use 'HydroScore' instead.
exact_mc	Exact method for p-value [Markov chains]
HydroScore	Dictionnaire
karlin	Karlin [p-value] [iid]
karlinMonteCarlo	Monte Carlo - Karlin [p-value]
karlinMonteCarlo_double	Monte Carlo - Karlin for real scores[p-value]
lindley	Lindley process
loadMatrixFromFile	Loads matrix from csv-File
loadScoreFromFile	Load score from file
localScore	Package for sequence analysis by local score
localScoreC	Local score
localScoreC_double	Local score for sequences of floating values
LongSeq	Deprecated. Use 'Seq1093' instead.
maxPartialSumd	Maximum of the partial sum [probability] [iid]
mcc	MCC [p-value] [iid]
MidSeq	Deprecated. Use 'Seq219' instead.
monteCarlo	Monte Carlo method [p-value]
monteCarlo_double	Monte Carlo method for real score case [p-value]
MySeqList	Deprecated. Use 'SeqListSCOPe' instead.
RealScores2IntegerScores	Convert a real scores vector into an integer scores vector
scoreDictionnary2probabilityVector	Check for missing scores values in the score distribution
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)
ShortSeq	Deprecated. Use 'Seq31' instead.
SJSyndrome.data	Stevens-Johnson syndrome data
stationary_distribution	Stationary distribution [Markov chains]
transmatrix2sequence	Sampling function for Markov chains