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: | 0.3.3 |
| Depends: | R (≥ 4.0), Matrix, PoissonBinomial, ShiftConvolvePoibin, utils, matrixStats |
| Imports: | maftools, data.table, parallel, RColorBrewer, methods |
| Suggests: | knitr, rmarkdown, RUnit, BiocStyle, dplyr, kableExtra, magick, qvalue, testthat (≥ 3.0.0) |
| Published: | 2025-12-19 |
| DOI: | 10.32614/CRAN.package.Rediscover |
| Author: | Juan A. Ferrer-Bonsoms [aut, cre], Laura Jareno [aut], Angel Rubio [aut] |
| 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 |
| Reference manual: | Rediscover.html , Rediscover.pdf |
| Vignettes: |
Rediscover (source, R code) |
| Package source: | Rediscover_0.3.3.tar.gz |
| Windows binaries: | r-devel: Rediscover_0.3.3.zip, r-release: Rediscover_0.3.3.zip, r-oldrel: Rediscover_0.3.3.zip |
| macOS binaries: | r-release (arm64): Rediscover_0.3.3.tgz, r-oldrel (arm64): Rediscover_0.3.3.tgz, r-release (x86_64): Rediscover_0.3.3.tgz, r-oldrel (x86_64): Rediscover_0.3.3.tgz |
| Old sources: | Rediscover archive |
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