Rediscover: Identify Mutually Exclusive Mutations (original) (raw)
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 |
| License: | Artistic-2.0 |
| NeedsCompilation: | no |
| Citation: | Rediscover citation info |
| Materials: | README NEWS |
| In views: | Omics |
| CRAN checks: | Rediscover results |
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