Fit timing of clonal peaks in cancer genome sequencing data

This function fits the timing of clonal peaks in cancer genome sequencing data using either a beta-binomial or binomial model.

Usage

fit(
  segments,
  mutations,
  purity,
  possible_k = c("2:1", "2:2", "2:0"),
  alpha = 0.05,
  min_mutations_number = 2,
  beta_binomial = FALSE,
  beta_binomial_disp = 0.01
)

Arguments

segments: A data frame containing segment information with columns chr, from, to, Major, and minor.
mutations: A data frame containing mutation information with columns chr, from, to, DP, and NV.
purity: A numeric value representing the tumor purity.
possible_k: A character vector of possible karyotypes in the format "Major:minor". Default is c("2:1", "2:2", "2:0").
alpha: A numeric value for the significance level. Default is 0.05.
min_mutations_number: An integer specifying the minimum number of mutations required for analysis. Default is 2.
beta_binomial: A logical value indicating whether to use the beta-binomial model. Default is FALSE.
beta_binomial_disp: A numeric value for the beta-binomial dispersion parameter. Default is 0.01.

Value

A list containing two tibbles: inference_results and summarized_results. Returns NULL if no results are obtained.