get_terminal_nodes: Identify which elements of a string are terminal nodes

In waldronlab/lefser: R implementation of the LEfSE method for microbiome biomarker discovery

Identify which elements of a string are terminal nodes

Description

A terminal node in a taxonomy does not have any child nodes. For example, a species is a terminal node if there are no subspecies or strains that belong to that species. This function identifies which elements of a vector are terminal nodes simply by checking whether that element appears as a substring in any other element of the vector.

Usage

get_terminal_nodes(string)

Arguments

string

A character vector of strings to check for terminal nodes

Value

A logical vector indicating which elements of the string are terminal nodes

Examples

# What does it do?
data("zeller14")
rownames(zeller14)[988:989]
get_terminal_nodes(rownames(zeller14)[988:989])
# How do I use it to keep only terminal nodes for a lefser analysis?
terminal_nodes <- get_terminal_nodes(rownames(zeller14))
zeller14sub <- zeller14[terminal_nodes, ]
# Then continue with your analysis!

waldronlab/lefser documentation built on Nov. 1, 2024, 9:02 p.m.