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
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