ranking: ranking the OTUs

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

Description

Ranking the importance of each taxa.

Usage

ranking(y, X, tree, cov = NULL,gamma,g.taxon.index,model = "binomial")

Arguments

y	Outcome of interest. It can be a disease indicator; =0 for controls, =1 for cases. Or it can be a quantitative trait. A vector with length n (number of observations).
X	OTU count table, row - n sample, column - q OTU
tree	Rooted phylogenetic tree of R class “phylo”
cov	Covariates. A matrix with dimension n by p (n :number of observation, p : number of covariates).
gamma	The best gamma selected by aMiSPU test.
g.taxon.index	g.taxon.index = 1 stands for weigted generalized taxon proportion; otherwise means unweighted generalized taxon proportion.
model	Use "gaussian" for a quantitative trait, and use "binomial" for a binary trait.

Value

A matrix containing the ranking score, the higher the more important.

Author(s)

Chong Wu

References

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 = ranking(Y,X, throat.tree,cov,gamma = 2, g.taxon.index =1)

MiSPU documentation built on May 1, 2019, 8:41 p.m.