ClonalSimData           Constructor for ClonalSimData
ClonalSimData-class     ClonalSimData Class
applyBiologicalNoise    Apply biological noise using Beta distribution
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,ClonalSimData,missing-method
                        Plot method for ClonalSimData
print.summary.ClonalSimData
                        Print summary method
show,ClonalSimData-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,ClonalSimData-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
