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: |
0.3.0 |
| Depends: |
R (≥ 4.0), Matrix, speedglm, PoissonBinomial, ShiftConvolvePoibin, utils, matrixStats |
| Imports: |
maftools, data.table, parallel, RColorBrewer, methods |
| Suggests: |
knitr, rmarkdown, RUnit, BiocStyle, BiocGenerics, dplyr, kableExtra, TCGAbiolinks, magick, stats, qvalue |
| Published: |
2021-10-06 |
| Author: |
Juan A. Ferrer-Bonsoms Developer [aut, cre],
Laura Jareno Developer [aut],
Angel Rubio User [aut, ctb] |
| Maintainer: |
Juan A. Ferrer-Bonsoms Developer <jafhernandez at tecnun.es> |
| License: |
Artistic-2.0 |
| NeedsCompilation: |
no |
| Citation: |
Rediscover citation info |
| Materials: |
README NEWS |
| CRAN checks: |
Rediscover results |