ranking: ranking the OTUs
In ChongWu-Biostat/MiSPU: Microbiome Based Sum of Powered Score (MiSPU) Tests

Description Usage Arguments Value Author(s) References Examples

Ranking the importance of each taxa.

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

`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.

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

Chong Wu

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

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)