Forward Genetic Simulation of Cancer Progresion with Epistasis


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Documentation for package ‘OncoSimulR’ version 2.0.1

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
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.
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.