scistreer (version 1.2.1)

run_scistree: Run the scistree workflow

Description

Run the scistree workflow

Usage

run_scistree(
  P,
  init = "UPGMA",
  ncores = 1,
  max_iter = 100,
  eps = 0.01,
  verbose = TRUE
)

Value

phylo A maximum-likelihood phylogeny

Arguments

P

matrix Genotype probability matrix (cell x mutation). Each entry is a probability (0-1) that the cell harbors the mutation

init

character Initialization strategy; UPGMA or NJ

ncores

integer Number of cores to use

max_iter

integer Maximum number of iterations

eps

numeric Tolerance threshold in likelihood difference for stopping

verbose

logical Verbosity

Examples

tree_small = run_scistree(P_small)