README.md

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

Log Ratio Tree Test

Differential Abundance Analysis for Microbiome data Incorporating Phylogeny. We call this methods LRTT（ Log Ratio Tree Test）.

Installation

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

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
• Tree.ratio.R : Tree ratio test based on the tree structure
• Tree.ratio.back.R: Correct steps of the tree ratio test.

Other function

• pow.fdr.R : calculate power and fdr with p.value
• Zig.pv.adj.R : metagenomeSeq::fitFeature *

Require

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

Example

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

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

p <- ncol(throat.otu.tab)
# throat.taxa.index <- Taxa.index(p, throat.tree)
colnames(throat.otu.tab) <- as.character(1:p)

throat.taxa.tab <- as.matrix(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.