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

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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.

Author
Chong Wu, Wei Pan
Date of publication
2016-03-18 00:08:39
Maintainer
Chong Wu <wuxx0845@umn.edu>
License
GPL-2
Version
1.0

View on CRAN

Man pages

correspLeaves
Finding the correspondence OTUs for each taxa
dd
The estimate of Dirichlet-multinomial distribution
Dirichlet
The Dirichlet Distribution
GUniFrac
Generalized UniFrac distances for comparing microbial...
MiSPU
microbiome based sum of powered score (MiSPU)
MiSPU-package
Microbiome Based Sum of Powered Score (MiSPU) Tests
ranking
ranking the OTUs
simulateData
OTU counts simulation
throat.meta
Meta data of the throat microbiome samples.
throat.otu.tab
OTU count table from 16S sequencing of the throat microbiome...
throat.tree
UPGMA tree of the OTUs from 16S sequencing of the throat...

Files in this package

MiSPU
MiSPU/src
MiSPU/src/Makevars
MiSPU/src/MiSPU.cpp
MiSPU/src/Makevars.win
MiSPU/src/RcppExports.cpp
MiSPU/NAMESPACE
MiSPU/data
MiSPU/data/throat.tree.rda
MiSPU/data/dd.rda
MiSPU/data/throat.meta.rda
MiSPU/data/throat.otu.tab.rda
MiSPU/R
MiSPU/R/GUniFrac.R
MiSPU/R/Ranking.R
MiSPU/R/RcppExports.R
MiSPU/R/MiSPU.R
MiSPU/R/MiSPUR.R
MiSPU/R/simulateData.R
MiSPU/MD5
MiSPU/DESCRIPTION
MiSPU/man
MiSPU/man/throat.otu.tab.Rd
MiSPU/man/throat.tree.Rd
MiSPU/man/throat.meta.Rd
MiSPU/man/GUniFrac.Rd
MiSPU/man/dd.Rd
MiSPU/man/ranking.Rd
MiSPU/man/MiSPU.Rd
MiSPU/man/correspLeaves.Rd
MiSPU/man/Dirichlet.Rd
MiSPU/man/simulateData.Rd
MiSPU/man/MiSPU-package.Rd