Rediscover: Identify Mutually Exclusive Mutations
An optimized method for identifying mutually exclusive genomic events. Its main contribution is a statistical analysis based on the Poisson-Binomial distribution that takes into account that some samples are more mutated than others. See [Canisius, Sander, John WM Martens, and Lodewyk FA Wessels. (2016) "A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence." Genome biology 17.1 : 1-17. <doi:10.1186/s13059-016-1114-x>]. The mutations matrices are sparse matrices. The method developed takes advantage of the advantages of this type of matrix to save time and computing resources.
| Version: | 0.3.2 |
| Depends: | R (≥ 4.0),Matrix,PoissonBinomial,ShiftConvolvePoibin, utils,matrixStats |
| Imports: | maftools,data.table, parallel,RColorBrewer, methods |
| Suggests: | knitr,rmarkdown,RUnit,BiocStyle,BiocGenerics,dplyr,kableExtra,magick, stats,qvalue |
| Published: | 2023-04-14 |
| DOI: | 10.32614/CRAN.package.Rediscover |
| Author: | Juan A. Ferrer-Bonsoms, Laura Jareno, and Angel Rubio |
| Maintainer: | Juan A. Ferrer-Bonsoms <jafhernandez at tecnun.es> |
| License: | Artistic-2.0 |
| NeedsCompilation: | no |
| Citation: | Rediscover citation info |
| Materials: | README,NEWS |
| In views: | Omics |
| CRAN checks: | Rediscover results[issues need fixing before 2025-12-17] |
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