get_gtree: Get a tidygraph tree with simplified mutational history.

In numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

Get a tidygraph tree with simplified mutational history.

Description

Specify either max_cost or n_cut. max_cost works similarly as h and n_cut works similarly as k in stats::cutree. The top-level normal diploid clone is always included.

Usage

get_gtree(tree, P, n_cut = 0, max_cost = 0)

Arguments

tree	phylo Single-cell phylogenetic tree
P	matrix Genotype probability matrix
n_cut	integer Number of cuts on the phylogeny to define subclones
max_cost	numeric Likelihood threshold to collapse internal branches

Value

tbl_graph Phylogeny annotated with branch lengths and mutation events

numbat documentation built on May 29, 2024, 1:29 a.m.