Forward Genetic Simulation of Cancer Progression with Epistasis

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Documentation for package ‘OncoSimulR’ version 2.18.0

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.