run_scistree: Run the scistree workflow

In scistreer: Maximum-Likelihood Perfect Phylogeny Inference at Scale

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
)

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

Value

phylo A maximum-likelihood phylogeny

Examples

tree_small = run_scistree(P_small)

scistreer documentation built on July 9, 2023, 5:54 p.m.