RDA_CCA: RDA or CCA calculate

In microbiota/amplicon: Statistics and visualization for microbiome data

RDA or CCA calculate

Description

Input otutab, metadata and environmental factors or phyloseq object; support Automatic select which method : RDA or CCA were used for analyze; output ggplot2 plot, data and statistical test result.

Usage

RDA_CCA(otu = otutab, map = metadata, ps = NULL, env = env, group = "Group")

Arguments

otu	OTU/ASV table;
map	Sample metadata;
env	environmental indicators table;
group	group ID;

Details

By default, input phyloseq object include metadata, otutab and env table

Value

list object including plot, stat table

Author(s)

Contact: Tao Wen [e-mail], Yong-Xin Liu [e-mail]

References

Yong-Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo & Yang Bai. A practical guide to amplicon and metagenomic analysis of microbiome data. Protein Cell, 2020(41), 1-16, DOI: https://doi.org/10.1007/s13238-020-00724-8

Jingying Zhang, Yong-Xin Liu, Na Zhang, Bin Hu, Tao Jin, Haoran Xu, Yuan Qin, Pengxu Yan, Xiaoning Zhang, Xiaoxuan Guo, Jing Hui, Shouyun Cao, Xin Wang, Chao Wang, Hui Wang, Baoyuan Qu, Guangyi Fan, Lixing Yuan, Ruben Garrido-Oter, Chengcai Chu & Yang Bai. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nature Biotechnology, 2019(37), 6:676-684, DOI: https://doi.org/10.1038/s41587-019-0104-4

Examples

RDA_CCA(otu=otutab, map=metadata, ps=NULL, env=env, group="Group")

microbiota/amplicon documentation built on April 30, 2023, 1:48 p.m.