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OncoSimulR (version 2.2.2)

Forward Genetic Simulation of Cancer Progresion with Epistasis

Description

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.

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Version

Version

2.2.2

License

GPL (>= 3)

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Maintainer

Ramon Diaz-Uriarte

Last Published

February 15th, 2017

Functions in OncoSimulR (2.2.2)

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