sublineage: Sub-lineage isolates on a phyologentic tree.

Description Usage Arguments

View source: R/sublineage_function.R

Description

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

Usage

1
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/rpinecone documentation built on Dec. 4, 2019, 1:14 p.m.