OncoSimulR: Forward Genetic Simulation of Cancer Progression with Epistasis

Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Tress, Conjunctive Bayesian Networks, and other tumor progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, and additive models) and plotting them.

Author
Ramon Diaz-Uriarte [aut, cre], Mark Taylor [ctb]
Date of publication
None
Maintainer
Ramon Diaz-Uriarte <rdiaz02@gmail.com>
License
GPL (>= 3)
Version
2.4.0
URLs

View on Bioconductor

Man pages

allFitnessEffects
Create fitness and mutation effects specification from...
evalAllGenotypes
Evaluate fitness/mutator effects of one or all possible...
example-missing-drivers
An example where there are intermediate missing drivers.
examplePosets
Example posets
examplesFitnessEffects
Examples of fitness effects
mcfLs
mcfLs simulation from the vignette
oncoSimulIndiv
Simulate tumor progression for one or more individuals,...
OncoSimulWide2Long
Convert the 'pops.by.time' component of an 'oncosimul' object...
plotClonePhylog
Plot a parent-child relationship of the clones.
plot.fitnessEffects
Plot fitnessEffects objects.
plotFitnessLandscape
Plot a fitness landscape.
plot.oncosimul
Plot simulated tumor progression data.
plotPoset
Plot a poset.
poset
Poset
rfitness
Generate random fitness.
samplePop
Obtain a sample from a population of simulations.
simOGraph
Simulate oncogenetic/CBN/XMPN DAGs.
to_Magellan
Create output for MAGELLAN.

Files in this package

OncoSimulR/DESCRIPTION
OncoSimulR/NAMESPACE
OncoSimulR/R
OncoSimulR/R/OncoSimulR.R
OncoSimulR/R/RcppExports.R
OncoSimulR/R/conversion-helpers.R
OncoSimulR/R/fitness_landscape_utils.R
OncoSimulR/R/from_genotype_utils.R
OncoSimulR/R/generate-random-trees.R
OncoSimulR/R/mutator.R
OncoSimulR/R/new-restrict.R
OncoSimulR/R/rfitness.R
OncoSimulR/R/stacked-plots.R
OncoSimulR/build
OncoSimulR/build/vignette.rds
OncoSimulR/data
OncoSimulR/data/ex_missing_drivers_b11.RData
OncoSimulR/data/ex_missing_drivers_b12.RData
OncoSimulR/data/examplePosets.RData
OncoSimulR/data/examplesFitnessEffects.RData
OncoSimulR/data/mcfLs.RData
OncoSimulR/inst
OncoSimulR/inst/CITATION
OncoSimulR/inst/NEWS
OncoSimulR/inst/doc
OncoSimulR/inst/doc/OncoSimulR.R
OncoSimulR/inst/doc/OncoSimulR.Rmd
OncoSimulR/inst/doc/OncoSimulR.html
OncoSimulR/inst/miscell
OncoSimulR/inst/miscell/example-binom-problems.cpp
OncoSimulR/man
OncoSimulR/man/OncoSimulWide2Long.Rd
OncoSimulR/man/allFitnessEffects.Rd
OncoSimulR/man/evalAllGenotypes.Rd
OncoSimulR/man/example-missing-drivers.Rd
OncoSimulR/man/examplePosets.Rd
OncoSimulR/man/examplesFitnessEffects.Rd
OncoSimulR/man/mcfLs.Rd
OncoSimulR/man/oncoSimulIndiv.Rd
OncoSimulR/man/plot.fitnessEffects.Rd
OncoSimulR/man/plot.oncosimul.Rd
OncoSimulR/man/plotClonePhylog.Rd
OncoSimulR/man/plotFitnessLandscape.Rd
OncoSimulR/man/plotPoset.Rd
OncoSimulR/man/poset.Rd
OncoSimulR/man/rfitness.Rd
OncoSimulR/man/samplePop.Rd
OncoSimulR/man/simOGraph.Rd
OncoSimulR/man/to_Magellan.Rd
OncoSimulR/src
OncoSimulR/src/BNB_nr.cpp
OncoSimulR/src/BNB_v1.cpp
OncoSimulR/src/Makevars
OncoSimulR/src/Makevars.win
OncoSimulR/src/OncoSimulR_init.c
OncoSimulR/src/RcppExports.cpp
OncoSimulR/src/bnb_common.cpp
OncoSimulR/src/bnb_common.h
OncoSimulR/src/common_classes.h
OncoSimulR/src/debug_common.h
OncoSimulR/src/new_restrict.cpp
OncoSimulR/src/new_restrict.h
OncoSimulR/src/new_restrict_former_print_utils.cpp
OncoSimulR/tests
OncoSimulR/tests/README_names.txt
OncoSimulR/tests/manual
OncoSimulR/tests/manual/README.txt
OncoSimulR/tests/manual/test.Z-driverCounts-long.R
OncoSimulR/tests/manual/test.Z-sample-only-last-long.R
OncoSimulR/tests/manual/test.Z-warning-mutPropGrowth-long.R
OncoSimulR/tests/manual/test.driverCounts-long.R
OncoSimulR/tests/manual/test.exercise-plotting-code-long.R
OncoSimulR/tests/manual/test.fitness-preds-long.R
OncoSimulR/tests/manual/test.mutPropGrowth-long.R
OncoSimulR/tests/manual/test.mutator-long.R
OncoSimulR/tests/manual/test.mutator-oncoSimulSample-long.R
OncoSimulR/tests/manual/test.oncoSimulSample-limits-long.R
OncoSimulR/tests/manual/test.per-gene-mutation-rates-long.R
OncoSimulR/tests/manual/test.poset-transformations-long.R
OncoSimulR/tests/manual/test.sample-prob-long.R
OncoSimulR/tests/manual/test.simuls-run-examples-long.R
OncoSimulR/tests/manual/test.warning-mutPropGrowth-long.R
OncoSimulR/tests/testthat
OncoSimulR/tests/testthat.R
OncoSimulR/tests/testthat/test.Z-all-fitness.R
OncoSimulR/tests/testthat/test.Z-driverCounts.R
OncoSimulR/tests/testthat/test.Z-mutator.R
OncoSimulR/tests/testthat/test.Z-oncoSimulIndiv.R
OncoSimulR/tests/testthat/test.Z-rfitness-landscape.R
OncoSimulR/tests/testthat/test.Z-sample-only-last.R
OncoSimulR/tests/testthat/test.Z-total-present-drivers.R
OncoSimulR/tests/testthat/test.all-fitness.R
OncoSimulR/tests/testthat/test.driverCounts.R
OncoSimulR/tests/testthat/test.epist-order-modules.R
OncoSimulR/tests/testthat/test.exercise-plotting-code.R
OncoSimulR/tests/testthat/test.exercise-rfitness.R
OncoSimulR/tests/testthat/test.exercise-to-Magellan.R
OncoSimulR/tests/testthat/test.fitness-preds.R
OncoSimulR/tests/testthat/test.genotFitness.R
OncoSimulR/tests/testthat/test.init-mutant.R
OncoSimulR/tests/testthat/test.modules-root-no-root.R
OncoSimulR/tests/testthat/test.mutPropGrowth.R
OncoSimulR/tests/testthat/test.mutator-oncoSimulSample.R
OncoSimulR/tests/testthat/test.mutator.R
OncoSimulR/tests/testthat/test.oncoSimulIndiv-miscell.R
OncoSimulR/tests/testthat/test.oncoSimulSample-failures.R
OncoSimulR/tests/testthat/test.oncoSimulSample-limits.R
OncoSimulR/tests/testthat/test.per-gene-mutation-rates.R
OncoSimulR/tests/testthat/test.plotFitnessLandscape.R
OncoSimulR/tests/testthat/test.poset-transformations.R
OncoSimulR/tests/testthat/test.sample-prob.R
OncoSimulR/tests/testthat/test.samplePop.R
OncoSimulR/tests/testthat/test.simuls-run-examples.R
OncoSimulR/tests/testthat/test.warning-mutPropGrowth.R
OncoSimulR/tests/testthat/test.wide2long.R
OncoSimulR/vignettes
OncoSimulR/vignettes/OncoSimulR.Rmd
OncoSimulR/vignettes/OncoSimulR.bib
OncoSimulR/vignettes/custom4.css
OncoSimulR/vignettes/gitHeadInfo.gin
OncoSimulR/vignettes/gitinfo.sty
OncoSimulR/vignettes/gitsetinfo.sty