Description Details Author(s) References Examples
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.
Package: | MiSPU |
Type: | Package |
Version: | 1.0 |
Date: | 2016-02-29 |
License: | GPL-2 |
Chong Wu, Wei Pan Maintainer: Chong Wu <wuxx0845@umn.edu>
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | 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
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