createTrees: Create a Tree Object

In HMPTrees: Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data

Description

This function creates a list tree objects of type 'phylo' for use in plotting the trees.

Usage

createTrees(data, samples = NULL, level = "genus", split = ".")

Arguments

data	A data frame in which each column contains the rdp read counts for every taxa given in the row names.
samples	Deprecated. Only send the columns in data to create.
level	The depth the tree creation will go down to (kingdom, phylum, class, order, family, genus, species, subspecies).
split	This is the character that separates the taxa levels in the row names.

Details

For 'level' k, p, c, o, f, g, s and ss can be used in place of kingdom, phylum, class, order, family, genus, species and subspecies respectively.

Value

A list of 'phylo' objects that can be passed to plotTree to plot them.

Author(s)

Berkley Shands, Patricio S. La Rosa, Elena Deych, William D. Shannon

Examples

	data(saliva)
	
	### Creates a tree for the 4th sample in 'Saliva'
	salivaTree <- createTrees(saliva[,4, drop=FALSE])

HMPTrees documentation built on May 2, 2019, 4:02 p.m.