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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("OncoSimulR")
AuthorRamon Diaz-Uriarte [aut, cre], Mark Taylor [ctb]
Bioconductor views BiologicalQuestion SomaticMutation
Date of publicationNone
MaintainerRamon Diaz-Uriarte <rdiaz02@gmail.com>
LicenseGPL (>= 3)
Version2.6.0
https://github.com/rdiaz02/OncoSimul, https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/

View on Bioconductor

Functions

allFitnessEffects Man page
allMutatorEffects Man page
benchmark_1 Man page
benchmark_1_0.05 Man page
benchmark_2 Man page
benchmark_3 Man page
diversityLOD Man page
diversityPOM Man page
evalAllGenotypes Man page
evalAllGenotypesFitAndMut Man page
evalAllGenotypesMut Man page
evalGenotype Man page
evalGenotypeFitAndMut Man page
evalGenotypeMut Man page
examplePosets Man page
examplesFitnessEffects Man page
ex_missing_drivers_b11 Man page
ex_missing_drivers_b12 Man page
LOD Man page
LOD.oncosimul2 Man page
LOD.oncosimulpop Man page
mcfLs Man page
oncoSimulIndiv Man page
oncoSimulPop Man page
oncoSimulSample Man page
OncoSimulWide2Long Man page
plotClonePhylog Man page
plot.evalAllGenotypes Man page
plot.evalAllGenotypesMut Man page
plot.fitnessEffects Man page
plotFitnessEffects Man page
plotFitnessLandscape Man page
plot.genotype_fitness_matrix Man page
plot.oncosimul Man page
plot.oncosimulpop Man page
plotPoset Man page
POM Man page
POM.oncosimul2 Man page
POM.oncosimulpop Man page
poset Man page
print.oncosimul Man page
print.oncosimulpop Man page
print.sampledGenotypes Man page
rfitness Man page
sampledGenotypes Man page
samplePop Man page
simOGraph Man page
summary.oncosimul Man page
summary.oncosimulpop Man page
to_Magellan Man page

Files

DESCRIPTION
NAMESPACE
R
R/LOD_POM.R R/OncoSimulR.R R/RcppExports.R R/conversion-helpers.R R/fitness_landscape_utils.R R/from_genotype_utils.R R/generate-random-trees.R R/mutator.R R/new-restrict.R R/rfitness.R R/stacked-plots.R
build
build/vignette.rds
data
data/benchmark_1.RData
data/benchmark_1_0.05.RData
data/benchmark_2.RData
data/benchmark_3.RData
data/ex_missing_drivers_b11.RData
data/ex_missing_drivers_b12.RData
data/examplePosets.RData
data/examplesFitnessEffects.RData
data/mcfLs.RData
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/OncoSimulR.R
inst/doc/OncoSimulR.Rmd
inst/doc/OncoSimulR.html
inst/miscell
inst/miscell/benchmark_1.R inst/miscell/benchmark_1_0.05.R inst/miscell/benchmark_2.R inst/miscell/benchmark_3.R
inst/miscell/example-binom-problems.cpp
inst/miscell/large_num_genes.R inst/miscell/large_num_genes_0.05.R inst/miscell/large_pop_size.R
man
man/OncoSimulWide2Long.Rd man/POM.Rd man/allFitnessEffects.Rd man/benchmarks.Rd man/evalAllGenotypes.Rd man/example-missing-drivers.Rd man/examplePosets.Rd man/examplesFitnessEffects.Rd man/mcfLs.Rd man/oncoSimulIndiv.Rd man/plot.fitnessEffects.Rd man/plot.oncosimul.Rd man/plotClonePhylog.Rd man/plotFitnessLandscape.Rd man/plotPoset.Rd man/poset.Rd man/rfitness.Rd man/samplePop.Rd man/simOGraph.Rd man/to_Magellan.Rd
src
src/BNB_nr.cpp
src/BNB_v1.cpp
src/Makevars
src/Makevars.win
src/OncoSimulR_init.c
src/RcppExports.cpp
src/accessible_genotypes.cpp
src/bnb_common.cpp
src/bnb_common.h
src/common_classes.h
src/debug_common.h
src/new_restrict.cpp
src/new_restrict.h
src/new_restrict_former_print_utils.cpp
tests
tests/README_names.txt
tests/manual
tests/manual/README.txt
tests/manual/test.Z-driverCounts-long.R tests/manual/test.Z-sample-only-last-long.R tests/manual/test.Z-warning-mutPropGrowth-long.R tests/manual/test.driverCounts-long.R tests/manual/test.exercise-plotting-code-long.R tests/manual/test.fitness-preds-long.R tests/manual/test.fixation-long.R tests/manual/test.mutPropGrowth-long.R tests/manual/test.mutator-long.R tests/manual/test.mutator-oncoSimulSample-long.R tests/manual/test.oncoSimulSample-limits-long.R tests/manual/test.per-gene-mutation-rates-long.R tests/manual/test.poset-transformations-long.R tests/manual/test.sample-prob-long.R tests/manual/test.simuls-run-examples-long.R tests/manual/test.warning-mutPropGrowth-long.R
tests/testthat
tests/testthat.R tests/testthat/test.LOD_POM.R tests/testthat/test.Z-all-fitness.R tests/testthat/test.Z-driverCounts.R tests/testthat/test.Z-mutator.R tests/testthat/test.Z-oncoSimulIndiv.R tests/testthat/test.Z-rfitness-landscape.R tests/testthat/test.Z-sample-only-last.R tests/testthat/test.Z-total-present-drivers.R tests/testthat/test.accessible_genotypes.R tests/testthat/test.all-fitness.R tests/testthat/test.driverCounts.R tests/testthat/test.epist-order-modules.R tests/testthat/test.exercise-plotting-code.R tests/testthat/test.exercise-rfitness.R tests/testthat/test.exercise-to-Magellan.R tests/testthat/test.fitness-preds.R tests/testthat/test.fixation.R tests/testthat/test.genotFitness.R tests/testthat/test.init-mutant.R tests/testthat/test.modules-root-no-root.R tests/testthat/test.mutPropGrowth.R tests/testthat/test.mutator-oncoSimulSample.R tests/testthat/test.mutator.R tests/testthat/test.oncoSimulIndiv-miscell.R tests/testthat/test.oncoSimulSample-failures.R tests/testthat/test.oncoSimulSample-limits.R tests/testthat/test.per-gene-mutation-rates.R tests/testthat/test.plotFitnessLandscape.R tests/testthat/test.poset-transformations.R tests/testthat/test.sample-prob.R tests/testthat/test.samplePop.R tests/testthat/test.simuls-run-examples.R tests/testthat/test.warning-mutPropGrowth.R tests/testthat/test.wide2long.R
vignettes
vignettes/OncoSimulR.Rmd
vignettes/OncoSimulR.bib
vignettes/custom4.css
vignettes/gitHeadInfo.gin
vignettes/gitinfo.sty
vignettes/gitsetinfo.sty
vignettes/preamble.tex
vignettes/relfunct.png
vignettes/relfunct.tex

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.