Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise

---

Documentation for package ‘ClonalSim’ version 1.0.0

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

applyBiologicalNoise	Apply biological noise using Beta distribution
ClonalSimData	Constructor for ClonalSimData
ClonalSimData-class	ClonalSimData Class
ClonalSimData-validity	ClonalSimData Class
getClonalStructure	Get clonal structure
getMetadata	Get metadata
getMutations	Get mutations data frame
getObservedVAF	Get observed VAF values (with sequencing noise)
getSimParams	Get simulation parameters
getTrueVAF	Get true VAF values (biological, without sequencing noise)
plot-method	Plot method for ClonalSimData
print.summary.ClonalSimData	Print summary method
show-method	Show method for ClonalSimData
simulateDepth	Simulate realistic sequencing depth
simulateSequencingReads	Simulate sequencing reads with binomial sampling
simulateTumor	Simulate tumor clonal evolution with realistic noise
summary-method	Summary method for ClonalSimData
toDataFrame	Export mutation data to data frame
toGRanges	Convert ClonalSimData to GRanges object
toPyClone	Convert to PyClone input format
toSciClone	Convert to SciClone input format
toVCF	Convert ClonalSimData to VCF format