Installation | Introduction | Estimation of the probabilities | Perform Co-ocurrence and mutually exclusive test | Using a single matrix | Using two matrices | Using a specific group of genes | Application of Rediscover to maftools | extra: compute the q-value | References | Session Information
Package: Rediscover 0.3.3
Rediscover: Identify Mutually Exclusive Mutations
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.
Authors:
Rediscover_0.3.3.tar.gz
Rediscover_0.3.3.zip(r-4.7)Rediscover_0.3.3.zip(r-4.6)Rediscover_0.3.3.zip(r-4.5)
Rediscover_0.3.3.tgz(r-4.6-any)Rediscover_0.3.3.tgz(r-4.5-any)
Rediscover_0.3.3.tar.gz(r-4.7-any)Rediscover_0.3.3.tar.gz(r-4.6-any)
Rediscover_0.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rediscover/json (API)
| # Install 'Rediscover' in R: |
| install.packages('Rediscover', repos = c('https://jferrer-b.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:c2ccd683b4. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 209 | ||
| source / vignettes | OK | 208 | ||
| linux-release-x86_64 | OK | 190 | ||
| macos-release-arm64 | OK | 192 | ||
| macos-oldrel-arm64 | OK | 164 | ||
| windows-devel | OK | 152 | ||
| windows-release | OK | 130 | ||
| windows-oldrel | OK | 136 | ||
| wasm-release | OK | 118 |
Exports:discoversomaticInteractionsgetMutexgetMutexABgetMutexGroupgetPM
Dependencies:clidata.tableDNAcopyfarvergluegtablelabelinglatticelifecyclemaftoolsMatrixmatrixStatspheatmapPoissonBinomialR6RColorBrewerRcppRhtslibrlangscalesShiftConvolvePoibinsurvivalviridisLite
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A_example data | A_example |
| A_Matrix data | A_Matrix |
| AMP_COAD data | AMP_COAD |
| B_example data | B_example |
| B_Matrix data | B_Matrix |
| discoversomaticInteractions | discoversomaticInteractions |
| getMutex function | getMutex |
| getMutexAB function | getMutexAB |
| getMutexGroup function | getMutexGroup |
| getPM function | getPM |
| PM_AMP_COAD data | PM_AMP_COAD |
| PM_COAD data | PM_COAD |
| An S4 class to store the probabilities | dim,PMatrix-method PMatrix PMatrix-class [,PMatrix,matrix,missing,ANY-method [,PMatrix,missing,numeric,ANY-method [,PMatrix,numeric,missing,ANY-method [,PMatrix,numeric,numeric,ANY-method |
| TCGA_COAD | TCGA_COAD |
