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)
#> Iter 2 -1615.02320811357, 0.061s
#> Iter 3 -1612.77216335478, 0.059s
#> Iter 4 -1611.12211209167, 0.058s
#> Iter 5 -1609.77582445369, 0.059s
#> Iter 6 -1608.45689338819, 0.059s
#> Iter 7 -1606.49695634113, 0.059s
#> Iter 8 -1606.49695634113, 0.059s