UPGMA tree of the OTUs from 16S sequencing of the throat microbiome samples.

Description

The OTU tree is constructed using UPGMA on the K80 distance matrice of the OTUs. It is a rooted tree of class "phylo".

Usage

data(throat.tree)

Format

The format is: chr "throat.tree"

Details

The OTUs are produced by the QIIME software. Singleton OTUs have been discarded.

Source

Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, et al. (2010) Disordered Microbial Communities in the Upper Respiratory Tract of Cigarette Smokers. PLoS ONE 5(12): e15216.

Examples

data(throat.tree)
## maybe str(throat.tree) ; plot(throat.tree) ...

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GUniFrac)
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-0
Loading required package: ape
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GUniFrac/throat.tree.Rd_%03d_medium.png", width=480, height=480)
> ### Name: throat.tree
> ### Title: UPGMA tree of the OTUs from 16S sequencing of the throat
> ###   microbiome samples.
> ### Aliases: throat.tree
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(throat.tree)
> ## maybe str(throat.tree) ; plot(throat.tree) ...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>