opt_phylo: Get optimal phylogeny

In AxelitoMartin/TumorEvolution:

Description

Get optimal phylogeny

Usage

opt_phylo(
  sampchain,
  projectname,
  K,
  numchain = 15,
  path = ".",
  burnin = 10,
  thin = 5,
  cutoff = 0.05,
  optK = NULL
)

Arguments

sampchain	An output object from the run_canpy() function.
projectname	Name of the project to save results.
K	Vector of the number of clones to be used.
numchain	Number of chains for the MCMC. Default is 15.
path	Relative path to where results should be saved. Default is current directory.
burnin	Burn-in period for the MCMC. Default is 10.
thin	Thining parameter for the MCMC. Default is 5.
cutoff	post configuration cutoff. Default is 0.05
optK	Optimal number of subclones. Default is NULL calculated from BIC

Value

Optimal phylogeny.

AxelitoMartin/TumorEvolution documentation built on Jan. 12, 2021, 2:43 a.m.