ZRChao / TEST.lrtt

Differential Abundance Analysis for Microbiome Incorporating Phylogeny

Tree.Ratio

Differential Abundance Analysis for Microbiome data Incorporating Phylogeny

Installation

# Install the released version from CRAN
install.packages("LTRR")

# Install the development version from GitHub
devtools::install_github("ZRChao/LTRR")

Contents

Simulation

• BIT.Sim.R for Multinomial(Binomial) Tree distribution
• DTM.Sim.R for Dirichlet Multinomial Tree distribution
• LNM.Sim.R for Logistical Normal Multinomial distribution
• ANCOM.Sim.R for Poission distribution (parameters set follow as ANCOM paper)

Tree relate function

• Tree.Sim.R : Tree simulation
• Taxa.index.R : relationship between leafs and internal nodes
• Prob.mult.R :calculate the probability of each leafs by multiple each probability along the branch
• Diff.otu.R : judge the probability of each node in two group equally or not
• Tree.ratio.R : Tree ratio test based on the tree structure

Other function

• pow.fdr.R : calculate power and fdr with p.value
• Zig.pv.adj.R : metagenomeSeq::fitFeature
• ancom.py : which is faster in python

Require

• ancom.R::ANCOM, metagenomeSeq::fitFeature, mvtnorm, gtools, rdirimult

Example

#You can see this in real data application of throat.R

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

p = ncol(throat.otu.tab)
throat.taxa.index <- Taxa.index(p, throat.tree)
throat.alltab <- cbind(throat.taxa.index*throat.otu.tab,  throat.otu.tab)
group <- throat.meta$SmokingState)

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)