| MiSPU-package {MiSPU} | R Documentation |
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.
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
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