# 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