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

Description Details Author(s) References Examples

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.

Details

Package: MiSPU
Type: Package
Version: 1.0
Date: 2016-02-29
License: GPL-2

Author(s)

Chong Wu, Wei Pan Maintainer: Chong Wu <wuxx0845@umn.edu>

References

Pan, W., et al.(2014) A powerful and adaptive association test for rare variants, Genetics, 197(4), 1081-95

Chong, W., Pan, W. (2015) An Adaptive Association Test for Microbiome Data, submitted.

Examples

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data(throat.otu.tab)
data(throat.tree)
data(throat.meta)

Y.tmp =throat.meta[,3]
Y = rep(0,dim(throat.meta)[1])
Y[Y.tmp=="Smoker"] = 1

cov.tmp = throat.meta[,c(10,12)]
cov = matrix(1,dim(throat.meta)[1],2)
cov[cov.tmp[,1]== "None",1] = 0
cov[cov.tmp[,2]== "Male",2] = 0

start.time = proc.time()
X = as.matrix(throat.otu.tab)

out = MiSPU(Y,X, throat.tree,cov,model =  "binomial", pow = c(2:8, Inf), n.perm = 1000)
out

ChongWu-Biostat/MiSPU documentation built on May 6, 2019, 11:18 a.m.