LRTT-package: Differential Abundance Analysis of Microbiome Data...

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

Description

LRTT simplified of Log Ratio Tree Test which do differential abundance based on the tree structure. The package here provides four data simulation function include with tree structure or not and test based on the tree with several other function to do analysis based on the tree.

The complete list of functions can be displayed with library(help = LRTT).

More information on LRTT can be found : https://github.com/ZRChao/LRTT

Details

Package: LRTT

Type: R package

Version: 0.1.0

Date: 2018-03-25

License: GPL-2

Author(s)

Chao ZHOU & Tao WANG

Maintainer : Chao ZHOU <[e-mail]>

References

Chao ZHOU, Tao WANG. (2018) Differential Abundance Analysis of Microbiome Data Incorporating Phylogeny (Under review).

Mandal, Siddhartha, et al. "Analysis of composition of microbiomes: a novel method for studying microbial composition." Microbial ecology in health and disease 26.1 (2015): 27663.

Xia, Fan, et al. "A logistic normal multinomial regression model for microbiome compositional data analysis." Biometrics 69.4 (2013): 1053-1063.

Torben Tvedebrink (2010). Overdispersion in allelic counts and theta-correction in forensic genetics. Theoretical Population Biology, 78(3), 200-210.

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 <- 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, result)

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