Extract evolutionary parameters from a MOBSTER fit — evolutionary

Mutation rate, time of emergence and selection coefficient of subclones are calculated. These values are calculated based on a population genetics model of tumour evolution see Williams et al. 2016 and 2018 for more details (Nature Genetics).

The mutation rate scaled by the probability of lineage survival $\beta$, $\mu/\beta$ is given by: $$\mu/\beta = M / (1/fmin - 1/fmax)$$ Where $fmin$ is the minimum VAF and $fmax$ is the maximum, and $M$ is the number of mutations between $fmin$ and $fmax$.

Selection is defined as the relative growth rates of host tumour cell populations ($\lambda h$) vs subclone ($\lambda s$): $$1+s=\lambda h / \lambda s$$

evolutionary_parameters(
  x,
  Nmax = 10^10,
  lq = 0.1,
  uq = 0.9,
  ploidy = 2,
  ncells = 2
)

Arguments

x	An object fit by MOBSTER.
Nmax	Time when tumour is sampled (in tumour doublings)
lq	lower quantile of VAF (0.05)
uq	upper quantile of VAF (0.95)
ploidy	of mutations (2)
ncells	Number of cells that accumulate mutations at each division 1 or 2, default is 1

Value

Mutation rate, time of emergence and selection coefficient of subclones.

Examples

data('fit_example', package = 'mobster')
evolutionary_parameters(fit_example)
#> # A tibble: 1 x 7
#>      mu exponent  time subclonefrequency subclonemutations cluster     s
#>   <dbl>    <dbl> <dbl>             <dbl>             <dbl> <chr>   <dbl>
#> 1  73.5     2.25  5.98             0.298              695. C2      0.177