sublineage: Sub-lineage isolates on a phyologentic tree.

In alexwailan/maria: Defines sub-lineages of a clonal expansion via an phylogenetic tree.

Description

Function to assign sub-lineages to isolates according to the structure of a rooted tree.

Usage

sublineage(dfs, tree, assign, igraph.tree, thresh, quiet)

Arguments

dfs	The depth-first search performed on the igraph tree.
tree	The rooted phylogenetic tree.
assign	Vector of Sub-lineage numbers corresponding to tips on a tree.
igraph.tree	Phylogenetic tree converted into a graph
thresh	SNP threshold for sub-lineage isolates on the phylogentic tree.
ntips	Number of tips on the phylogenetic tree.

alexwailan/maria documentation built on Sept. 29, 2020, 9:37 a.m.