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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 |
Reference manual: | Rediscover.pdf |
Vignettes: |
Rediscover |
Package source: | Rediscover_0.3.2.tar.gz |
Windows binaries: | r-devel: Rediscover_0.3.2.zip, r-release: Rediscover_0.3.2.zip, r-oldrel: Rediscover_0.3.2.zip |
macOS binaries: | r-release (arm64): Rediscover_0.3.2.tgz, r-oldrel (arm64): Rediscover_0.3.2.tgz, r-release (x86_64): Rediscover_0.3.2.tgz, r-oldrel (x86_64): Rediscover_0.3.2.tgz |
Old sources: | Rediscover archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.