get_tree: Get a clonal tree from a configuration matrix

In PMBio/cardelino: Clone Identification from Single Cell Data

Get a clonal tree from a configuration matrix

Description

Get a clonal tree from a configuration matrix

Usage

get_tree(Config, P = NULL, strictness = "lax")

Arguments

Config	variant x clone matrix of binary values. The clone-variant configuration, which encodes the phylogenetic tree structure. This is the output Z of Canopy
P	a one-column numeric matrix encoding the (observed or estimated) prevalence (or frequency) of each clone
strictness	character(1), a character string defining the strictness of the function if there are all-zero rows in the Config matrix. If "lax" then the function silently drops all-zero rows and proceeds. If "warn" then the function warns of dropping all-zero rows and proceeds. If "error" then the function throws an error is all-zero rows are detected.

Details

Output tree may be nonsensical if the input Config matrix does not define a coherent tree structure.

Value

An object of class "phylo" describing the tree structure. The output object also contains an element "sna" defining the clustering of variants onto the branches of the tree, and if P is non-null it also contains VAF (variant allele frequency), CCF (cell clone fraction) and clone prevalence values (computed from the supplied P argument).

Author(s)

Davis McCarthy

Examples

Configk3 <- matrix(c(
    rep(0, 15), rep(1, 8), rep(0, 7), rep(1, 5), rep(0, 3),
    rep(1, 7)
), ncol = 3)
tree_k3 <- get_tree(Config = Configk3, P = matrix(rep(1 / 3, 3), ncol = 1))
plot_tree(tree_k3)

PMBio/cardelino documentation built on Nov. 21, 2022, 4:52 a.m.