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Get evolutionary parameters from the model

Source: R/evolutionary_parameters.R
evo_params.Rd

Code of those functions is only re-formatted code from MOBSTER R package by Caravagna, Williams et al. https://github.com/caravagnalab/mobster

Usage

get_mutation_rates(object, ...)

# S3 method for cevodata
get_mutation_rates(object, models_name = "powerlaw_fixed", ...)

# S3 method for tbl_df
get_mutation_rates(object, ...)

get_selection_coefficients(object, ...)

# S3 method for cevodata
get_selection_coefficients(
  object,
  models_name = "powerlaw_fixed_subclones",
  Nmax = 10^10,
  ...
)

# S3 method for tbl_df
get_selection_coefficients(object, Nmax = 10^10, ...)

Arguments

object

cevodata object or models tibble

...

other arguments

models_name

models_name

Nmax

Time when tumour is sampled (in tumour doublings)

Functions

  • get_mutation_rates(): Get mutation rates by Williams Use ...

  • get_mutation_rates(cevodata): Get mutation rates by Williams

  • get_mutation_rates(tbl_df): Get mutation rates by Williams

  • get_selection_coefficients(): Get subclonal selection coefficients Williams

    Use properties of subclone fit to calculate selection intensity, selection is defined as the relative growth rates of host tumour cell populations (\(\lambda h\)) vs subclone (\(\lambda s\)): $$1+s=\lambda h / \lambda s$$

  • get_selection_coefficients(cevodata): Get subclonal selection coefficients Williams

  • get_selection_coefficients(tbl_df): Get subclonal selection coefficients Williams