In caravagnalab/mobster: MOBSTER - Model-based tumour subclonal deconvolution

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(mobster)
library(tidyr)
library(dplyr)

Population Genetics statistics can be extracted from a MOBSTER model.

data('fit_example', package = 'mobster')
print(fit_example$best)

evolutionary_parameters(fit_example)

The mutation rate mu (cell division units) scaled by the probability of lineage survival $\beta$, $\mu/\beta$, is given by: [ \mu/\beta = \dfrac{M} {(\frac{1}{f_\text{min}} - \frac{1}{f_\text{max}})} ] Where $f_\text{min}$ is the minimum VAF and $f_\text{max}$ is the maximum, and $M$ is the number of mutations between $f_\text{min}$ and $f_\text{max}$.

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

The mathematical details of these computations are described in the main paper, and baesd on the population genetics model of tumour evolutionin Williams et al. 2016 and 2018 (Nature Genetics).

caravagnalab/mobster documentation built on March 25, 2023, 3:40 p.m.