localScore v1.0.6
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Package for Sequence Analysis by Local Score
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) <https://hal.archives-ouvertes.fr/hal-00714174> ; S. Karlin and S. Altschul (1990) <https://www.pnas.org/content/87/6/2264> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.archives-ouvertes.fr/hal-00937529v1> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).
Functions in localScore
| Name | Description | |
| MidSeq | Protein sequence | |
| CharSequences2ScoreSequences | Convert several character sequences into score sequences | |
| CharSequence2ScoreSequence | Convert a character sequence into a score sequence | |
| karlinMonteCarlo_double | Monte Carlo - Karlin for real scores[p-value] | |
| karlinMonteCarlo | Monte Carlo - Karlin [p-value] | |
| loadMatrixFromFile | Loads matrix from csv-File | |
| scoreSequences2probabilityVector | Empirical distribution from sequences | |
| lindley | Lindley process | |
| sequences2transmatrix | Transition matrix from sequence(s) | |
| ShortSeq | Short protein sequence | |
| stationary_distribution | Stationary distribution [Markov chains] | |
| MySeqList | Several sequences | |
| transmatrix2sequence | Sampling function for Markov chains | |
| localScore-package | Package for sequence analysis by local score | |
| loadScoreFromFile | Load score from file | |
| RealScores2IntegerScores | Convert a real scores vector into an integer scores vector | |
| scoreDictionnary2probabilityVector | Check for missing scores values in the score distribution | |
| monteCarlo_double | Monte Carlo method for real score case [p-value] | |
| localScoreC_double | Local score for sequences of floating values | |
| dico | Dictionnaire | |
| daudin | Daudin [p-value] [iid] | |
| localScoreC | Local score | |
| automatic_analysis | Automatic analysis | |
| karlin | Karlin [p-value] [iid] | |
| exact_mc | Exact method for p-value [Markov chains] | |
| mcc | MCC [p-value] [iid] | |
| monteCarlo | Monte Carlo method [p-value] | |
| LongSeq | Long protein sequence | |
| No Results! | ||
Vignettes of localScore
| Name | ||
| localScorePackageDocumentation.Rmd | ||
| No Results! | ||
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Details
| Type | Package |
| Date | 2021-02-24 |
| Copyright | See the file COPYRIGHTS for various embedded Eigen library copyright details |
| License | GPL (>= 2) | file LICENSE |
| LinkingTo | Rcpp |
| RoxygenNote | 7.1.1 |
| LazyData | true |
| Encoding | UTF-8 |
| SystemRequirements | C++11 |
| VignetteBuilder | knitr |
| NeedsCompilation | yes |
| Packaged | 2021-02-24 10:24:09 UTC; drobelin |
| Repository | CRAN |
| Date/Publication | 2021-02-24 22:40:23 UTC |
| suggests | knitr , rmarkdown , testthat (>= 2.1.0) |
| depends | R (>= 3.2.0) |
| imports | Rcpp (>= 0.12.16) , utils |
| Contributors | Sbastien Djean, Sebastian Simon, Sabine Mercier, The authors of Eigen the library for the included version of Eigen |
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