- code clean-up, unnecessary dependencies removed
- subclones can be fitted using CliP (Jiang et al., 2021) (
fit_subclones(method = "CliP")). This option requires that the Apptainer is installed. CliP container image can be build withbuild_clip_container()
- fit_powerlaw_tail_fixed() has a bootstrap option
- cevomod is integrated with a helper readthis package, designed for bulk reading of variant files from algorithms such as Mutect2, Strelka, ASCAT, or FACETS, in the cevomod-friendly data format. Objects returned by
readthis::read_*()functions can be added to the cevodata object using a generaladd_data()function.
- cevomod functions can no utilize VAF or CCF (Cancer Cell Fraction) as a measure of mutation frequency. CCF is calculated using the formula introduced in Dentro et al. Principles of Reconstructing the Subclonal Architecture of Cancers (2015)
- cevodata export to CliP implemented
- cevodata class implementation
- fitting the power-law tails with exponent equal to 2 using
$M(f) \sim 1/f$ statistic - fitting the power-law tails with optimized exponent
- fitting subclones using mclust
- fitting subclones using BMix
- calculation of the evolutionary parameters using the Williams et al. (2018) equations and the MOBSTER code (Caravagna et al. (2020))