# Forward Genetic Simulation of Cancer Progression with Epistasis

## Documentation for package ‘OncoSimulR’ version 3.0.0

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

## Help Pages

allFitnessEffects | Create fitness and mutation effects specification from restrictions, epistasis, and order effects.
allMutatorEffects | Create fitness and mutation effects specification from restrictions, epistasis, and order effects.
benchmark_1 | Summary results from some benchmarks reported in the vignette.
benchmark_1_0.05 | Summary results from some benchmarks reported in the vignette.
benchmark_2 | Summary results from some benchmarks reported in the vignette.
benchmark_3 | Summary results from some benchmarks reported in the vignette.
diversityLOD | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
diversityPOM | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
evalAllGenotypes | Evaluate fitness/mutator effects of one or all possible genotypes.
evalAllGenotypesFitAndMut | Evaluate fitness/mutator effects of one or all possible genotypes.
evalAllGenotypesMut | Evaluate fitness/mutator effects of one or all possible genotypes.
evalGenotype | Evaluate fitness/mutator effects of one or all possible genotypes.
evalGenotypeFitAndMut | Evaluate fitness/mutator effects of one or all possible genotypes.
evalGenotypeMut | Evaluate fitness/mutator effects 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.
LOD | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
LOD.oncosimul2 | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
LOD.oncosimulpop | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
Magellan_stats | Create output for MAGELLAN and obtain MAGELLAN statistics.
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.evalAllGenotypes | Plot a fitness landscape.
plot.evalAllGenotypesMut | Plot a fitness landscape.
plot.fitnessEffects | Plot fitnessEffects objects.
plot.genotype_fitness_matrix | Plot a fitness landscape.
plot.oncosimul | Plot simulated tumor progression data.
plot.oncosimulpop | Plot simulated tumor progression data.
plotClonePhylog | Plot a parent-child relationship of the clones.
plotFitnessLandscape | Plot a fitness landscape.
plotPoset | Plot a poset.
POM | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
POM.oncosimul2 | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
POM.oncosimulpop | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
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.
print.sampledGenotypes | Obtain a sample from a population of simulations.
rfitness | Generate random fitness.
sampledGenotypes | Obtain a sample from a population of simulations.
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.
to_Magellan | Create output for MAGELLAN and obtain MAGELLAN statistics.
woAntibS | Runs from simulations of frequency-dependent examples shown in the vignette.