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MiSPU (version 1.0)

Microbiome Based Sum of Powered Score (MiSPU) Tests

Description

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.

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Version

Install

install.packages('MiSPU')

Monthly Downloads

106

Version

1.0

License

GPL-2

Maintainer

Last Published

March 17th, 2016

Functions in MiSPU (1.0)

MiSPU

microbiome based sum of powered score (MiSPU)
correspLeaves

Finding the correspondence OTUs for each taxa
ranking

ranking the OTUs
throat.otu.tab

OTU count table from 16S sequencing of the throat microbiome samples.
DirMultOutput

The estimate of Dirichlet-multinomial distribution
throat.tree

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

Meta data of the throat microbiome samples.
Dirichlet

The Dirichlet Distribution
simulateData

OTU counts simulation
MiSPU-package

Microbiome Based Sum of Powered Score (MiSPU) Tests