throat.otu.tab: OTU count table from 16S sequencing of the throat microbiome...

In MiSPU: Microbiome Based Sum of Powered Score (MiSPU) Tests

Description

It is part of a microbiome data set for studying the effect of smoking on the upper respiratory tract microbiome. The original data set contains samples from both throat and nose microbiomes, and from both body sides. This data set comes from the throat microbiome of left body side. It contains 60 subjects consisting of 32 nonsmokers and 28 smokers.

Usage

data(throat.otu.tab)

Format

The format is: chr "throat.otu.tab"

Details

The OTU table is 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.otu.tab)
## maybe str(throat.otu.tab) ; plot(throat.otu.tab) ...

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Loading required package: ape
Loading required package: aSPU
Loading required package: gee
Loading required package: MASS
Loading required package: mvtnorm
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.1-1 (2017-07-02) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: maps
Loading required package: matrixStats
Loading required package: cluster

Attaching package: 'cluster'

The following object is masked from 'package:maps':

    votes.repub

MiSPU documentation built on May 1, 2019, 8:41 p.m.