# Forward Genetic Simulation of Cancer Progresion with Epistasis

## Documentation for package ‘OncoSimulR’ version 2.2.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

allFitnessEffects | Create fitness effects specification from restrictions, epistasis, and order effects.
evalAllGenotypes | Evaluate fitness of one or all possible genotypes.
evalGenotype | Evaluate fitness of one or all possible genotypes.
examplePosets | Example posets
examplesFitnessEffects | Examples of fitness effects
ex_missing_drivers_b11 | An example where there are intermediate missing drivers.
ex_missing_drivers_b12 | An example where there are intermediate missing drivers.
mcfLs | mcfLs simulation from the vignette
oncoSimulIndiv | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
oncoSimulPop | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
oncoSimulSample | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
OncoSimulWide2Long | Convert the 'pops.by.time' component of an 'oncosimul' object into "long" format.
plot.fitnessEffects | Plot fitnessEffects objects.
plot.oncosimul | Plot simulated tumor progression data.
plot.oncosimulpop | Plot simulated tumor progression data.
plotClonePhylog | Plot a phylogeny of the clones.
plotPoset | Plot a poset.
poset | Poset
print.oncosimul | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
print.oncosimulpop | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
samplePop | Obtain a sample from a population of simulations.
simOGraph | Simulate oncogenetic/CBN/XMPN DAGs.
summary.oncosimul | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
summary.oncosimulpop | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.