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 ($\lambda s$): $$1+s=\lambda h / \lambda s$$

Usage

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 × 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