Tree.ratio: Tree.ratio

In ZRChao/LRTT: Differential Abundance Analysis for Microbiome data incorpating phylogeney

Description

Tree ratio test based on the tree.

Usage

Tree.ratio(p, tree, taxa.index, alltab, group = c(1:N))

Arguments

p	the number of OTU
tree	the tree structure, phylo object
taxa.index	matrix return by Taxa.index
alltab	the count data matrix
group	the class of each sample

Value

A list data

alltab	data after test by prune the tree
taxa.pvalue	pvalue of the internal nodes
taxa.dif	differential internal nodes
otu.dif	differential OTU before corrected

See Also

Taxa.index

Examples

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

p <- ncol(throat.otu.tab)
# throat.taxa.index <- Taxa.index(p, throat.tree)
data(throat.taxa.index )
colnames(throat.otu.tab) <- as.character(1:p)
throat.taxa.tab <- throat.otu.tab %*% throat.taxa.index
  
throat.alltab <- cbind(throat.taxa.tab,  throat.otu.tab)
group <- throat.meta$SmokingStatus

result <- Tree.ratio(p, throat.tree, throat.taxa.index, throat.alltab, group)

throat.detected <- Tree.ratio.back(p, throat.tree, throat.taxa.index, results, group)

ZRChao/LRTT documentation built on May 17, 2019, 6:36 p.m.