throat.tree

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

datasets

There is an increasing interest in investigating how the compositions of microbial communities are associated with human health and disease. In this package, we present a novel global testing method called aMiSPU, that is highly adaptive and thus high powered across various scenarios, alleviating the issue with the choice of a phylogenetic distance. Our simulations and real data analysis demonstrated that aMiSPU test was often more powerful than several competing methods while correctly controlling type I error rates.

Chong Wu

MiSPU

Microbiome Based Sum of Powered Score (MiSPU) Tests

throat.tree function

Format

 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.

Source



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


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

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Source

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Examples