API for OncoSimulR
Forward Genetic Simulation of Cancer Progression with Epistasis
| Global functions | |
|---|---|
| BNB_Algo5 | Source code |
| LOD | Man page Source code |
| LOD.internal | Source code |
| LOD.internal_pre_2.9.2 | Source code |
| LOD.oncosimul2 | Man page Source code |
| LOD.oncosimul2_pre_2.9.2 | Source code |
| LOD.oncosimulpop | Man page Source code |
| LOD_as_path | Source code |
| Magellan_draw | Source code |
| Magellan_stats | Man page Source code |
| Magellan_stats_former | Source code |
| OTtoPoset | Source code |
| OncoSimulWide2Long | Man page Source code |
| POM | Man page Source code |
| POM.internal | Source code |
| POM.oncosimul2 | Man page Source code |
| POM.oncosimulpop | Man page Source code |
| POM_pre_2.9.2 | Source code |
| accessibleGenotypes | Source code |
| accessibleGenotypes_former | Source code |
| addIntID.epist.order | Source code |
| add_noise | Source code |
| adjmat.to.restrictTable | Source code |
| allFitnessEffects | Man page Source code |
| allFitnessORMutatorEffects | Source code |
| allGenotypes_to_matrix | Source code |
| allMutatorEffects | Man page Source code |
| allNamedGenes | Source code |
| benchmark_1 | Man page |
| benchmark_1_0.05 | Man page |
| benchmark_2 | Man page |
| benchmark_3 | Man page |
| check.gm | Source code |
| checkProperFullAdjMat | Source code |
| checkProperMinimalAdjMat | Source code |
| checkProperOTAdjMat | Source code |
| checkRT | Source code |
| closest_time | Source code |
| connect | Source code |
| connectIndiv | Source code |
| convertRestrictTable | Source code |
| countGenesFe | Source code |
| create.drivers.by.time | Source code |
| create_eq_ref | Source code |
| detectionProbCheckParse | Source code |
| diversityLOD | Man page Source code |
| diversityPOM | Man page Source code |
| epist.order.element | Source code |
| epist.order.to.pairs.modules | Source code |
| evalAllGenotypes | Man page Source code |
| evalAllGenotypesFitAndMut | Man page Source code |
| evalAllGenotypesMut | Man page Source code |
| evalAllGenotypesORMut | Source code |
| evalGenotype | Man page Source code |
| evalGenotypeFitAndMut | Man page Source code |
| evalGenotypeMut | Man page Source code |
| evalGenotypeORMut | Source code |
| evalRGenotype | Source code |
| evalRGenotypeAndMut | Source code |
| ex_missing_drivers_b11 | Man page |
| ex_missing_drivers_b12 | Man page |
| examplePosets | Man page |
| examplesFitnessEffects | Man page |
| fast_peaks | Source code |
| faster_accessible_genotypes_R | Source code |
| filter_inaccessible | Source code |
| filter_phylog_df_LOD | Source code |
| fitnessEffectsToIgraph | Source code |
| fl_generate_binary | Source code |
| fl_statistics_binary | Source code |
| geneCounts | Source code |
| geneModuleNull | Source code |
| generateAllGenotypes | Source code |
| generate_matrix_genotypes | Source code |
| genot2AdjMat | Source code |
| genot_fitness_to_epistasis | Source code |
| genot_max | Source code |
| genot_to_adj_mat | Source code |
| genot_to_adj_mat_R | Source code |
| genotypeLabel | Source code |
| get.gene.counts | Source code |
| get.mut.vector | Source code |
| get.the.time.for.sample | Source code |
| getGeneIDNum | Source code |
| getNamesID | Source code |
| get_magellan_binaries | Source code |
| gm.to.geneModuleL | Source code |
| gtm2 | Source code |
| is_null_na | Source code |
| list.of.deps | Source code |
| list_g_matches_fixed | Source code |
| matchGeneIDs | Source code |
| mcfLs | Man page |
| myhsvcols | Source code |
| mysplitb | Source code |
| nem_transitive.closure | Source code |
| nem_transitive.reduction | Source code |
| nice.vector.eo | Source code |
| nr_BNB_Algo5 | Source code |
| nr_oncoSimul.internal | Source code |
| oe.to.df | Source code |
| oncoSimul.internal | Source code |
| oncoSimulIndiv | Man page Source code |
| oncoSimulPop | Man page Source code |
| oncoSimulSample | Man page Source code |
| peak_valley | Source code |
| peaksLandscape | Source code |
| phcl_from_lod | Source code |
| phylogClone | Source code |
| plot.evalAllGenotypes | Man page |
| plot.evalAllGenotypesMut | Man page |
| plot.fitnessEffects | Man page Source code |
| plot.genotype_fitness_matrix | Man page |
| plot.oncosimul | Man page Source code |
| plot.oncosimulpop | Man page Source code |
| plot.stacked2 | Source code |
| plot.stream2 | Source code |
| plotClonePhylog | Man page Source code |
| plotClonesSt | Source code |
| plotDrivers0 | Source code |
| plotFitnessEffects | Man page |
| plotFitnessLandscape | Man page Source code |
| plotPoset | Man page Source code |
| plotShannon | Source code |
| poset | Man page |
| poset.to.restrictTable | Source code |
| posetToGraph | Source code |
| print.oncosimul | Man page Source code |
| print.oncosimulpop | Man page Source code |
| print.sampledGenotypes | Man page Source code |
| relabelLogaxis | Source code |
| rfitness | Man page Source code |
| samplePop | Man page Source code |
| sampledGenotypes | Man page Source code |
| shannonI | Source code |
| simOGraph | Man page Source code |
| summary.oncosimul | Man page Source code |
| summary.oncosimulpop | Man page Source code |
| thin.pop.data | Source code |
| to.long.epist.order | Source code |
| to.long.rt | Source code |
| to.pairs.modules | Source code |
| to_Fitness_Matrix | Source code |
| to_Magellan | Man page Source code |
| to_genotFitness_std | Source code |
| which_N_at_T | Source code |
| wrap_accessibleGenotypes | Source code |
| wrap_accessibleGenotypes_former | Source code |
| xlim.pop.data | Source code |
