OncoSimulR v2.2.2
Forward Genetic Simulation of Cancer Progresion with Epistasis
Functions for forward population genetic simulation in
asexual populations, with special focus on cancer progression.
Fitness can be an arbitrary function of genetic interactions between
multiple genes or modules of genes, including epistasis, order
restrictions in mutation accumulation, and order effects. Simulations
use continuous-time models and can include driver and passenger genes
and modules. Also included are functions for simulating random DAGs
of the type found in Oncogenetic Tress, Conjunctive Bayesian Networks,
and other tumor progression models, and for plotting and sampling from
single or multiple realizations of the simulations, including
single-cell sampling, as well as functions for plotting the true
phylogenetic relationships of the clones.
Functions in OncoSimulR
| Name | Description | |
| plot.fitnessEffects | Plot fitnessEffects objects. | |
| mcfLs | mcfLs simulation from the vignette | |
| example-missing-drivers | An example where there are intermediate missing drivers. | |
| poset | Poset | |
| plotPoset | Plot a poset. | |
| allFitnessEffects | Create fitness effects specification from restrictions, epistasis, and order effects. | |
| OncoSimulWide2Long | Convert the pops.by.time component of an oncosimul object into "long" format. | |
| examplePosets | Example posets | |
| oncoSimulIndiv | Simulate tumor progression for one or more individuals, optionally returning just a sample in time. | |
| plotClonePhylog | Plot a phylogeny of the clones. | |
| samplePop | Obtain a sample from a population of simulations. | |
| plot.oncosimul | Plot simulated tumor progression data. | |
| evalAllGenotypes | Evaluate fitness of one or all possible genotypes. | |
| simOGraph | Simulate oncogenetic/CBN/XMPN DAGs. | |
| examplesFitnessEffects | Examples of fitness effects | |
| No Results! | ||
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Details
| Type | Package |
| Date | 2016-04-14 |
| biocViews | BiologicalQuestion, SomaticMutation |
| License | GPL (>= 3) |
| URL | https://github.com/rdiaz02/OncoSimul, https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/ |
| BugReports | https://github.com/rdiaz02/OncoSimul/issues |
| LinkingTo | Rcpp |
| VignetteBuilder | knitr |
| depends | base (>= 3.1.0) , R (>= 3.1.0) |
| suggests | BiocStyle , knitr , Oncotree , testthat |
| imports | data , data.table , graph , grDevices , gtools , igraph , methods , parallel , RColorBrewer , Rcpp (>= 0.11.1) , Rgraphviz |
| Contributors | Ramon Diaz-Uriarte, Mark Taylor |
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