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Rediscover

Identify Mutually Exclusive Mutations

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About

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.

Citation Rediscover citation info

Key Metrics

Version 0.3.1
R ≥ 4.0
Published 2023-02-12 492 days ago
Needs compilation? no
License Artistic-2.0
CRAN checks Rediscover results

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Maintainer

Maintainer

Juan A. Ferrer-Bonsoms

Authors

Juan A. Ferrer-Bonsoms
Laura Jareno
Angel Rubio

Material

README
NEWS
Reference manual
Package source

Vignettes

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macOS

r-release

arm64

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arm64

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x86_64

r-oldrel

x86_64

Windows

r-develnot available

x86_64

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x86_64

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x86_64

Old Sources

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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
magick
stats
qvalue