/LRTT

Differential Abundance Analysis for Microbiome data Incorporating Phylogeny

Primary LanguageR

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)