NEWS
ClonalSim 0.99.6
Bug Fixes
- Removed incorrect
seed parameter from simulateTumor() examples in README;
use set.seed() before calling the function for reproducibility
- Removed unnecessary
library(ggplot2) calls from README, vignette, and
documentation — ggplot2 is already imported via NAMESPACE and loads
automatically with the package
ClonalSim 0.99.0
New Features
- Initial Bioconductor submission
- Simulate tumor clonal evolution with hierarchical structure
- Realistic biological noise model using Beta distribution
- Technical sequencing noise with negative binomial depth variation
- Binomial sampling for stochastic read counts
- Sequencing error simulation (Illumina-like)
- S4 class for simulation results
- Export to GRanges and VCF formats
- Comprehensive visualization suite:
- VAF distribution plots
- Clonal matrix heatmap
- Fish plot for temporal evolution
- Modular, configurable noise parameters
- Full Roxygen2 documentation
- Comprehensive vignettes for educational use
- Unit tests with >80% coverage
Implementation Details
- Biological heterogeneity modeled with Beta distribution
- Depth overdispersion with negative binomial distribution
- Realistic read sampling with binomial distribution
- Configurable evolutionary hierarchies
- Support for founder, shared, and private mutations
Future Plans
- Copy number alteration (CNA) simulation
- Loss of heterozygosity (LOH) support
- Subclonal CNA modeling
- Integration with mutational signature analysis tools