MicroTest: Beta diversity statistics by adonis/anosim/MRPP in all groups

In microbiota/amplicon: Statistics and visualization for microbiome data

Beta diversity statistics by adonis/anosim/MRPP in all groups

Description

Input phyloseq object, test method and distance type

Usage

MicroTest(
  otu = NULL,
  map = NULL,
  ps = ps,
  group = "Group",
  Micromet = "MRPP",
  dist = "bray"
)

Arguments

otu	OTU/ASV table;
map	Sample metadata;
ps	alternative input;
group	group ID;
Micromet	statistics default by adonis, alternative anosim or MRPP;
dist	distance type, including "unifrac" "wunifrac" "dpcoa" "jsd" "manhattan" "euclidean" "canberra" "bray" "kulczynski" "jaccard" "gower" "altGower" "morisita" "horn" "mountford" "raup" "binomial" "chao" "cao" "w" "-1" "c" "wb" "r" "I" "e" "t" "me" "j" "sor" "m" "-2" "co";
tree	tree/nwk file;
method	DCA, CCA, RDA, NMDS, MDS, PCoA, PCA, LDA;
pvalue.cutoff	Pvalue threshold, default in 0.05;

Details

By default, input phyloseq object include metadata and otutab The available diversity indices include the following:

• most used indices: bray unifrac wunifrac

• other used indices: dpcoa jsd manhattan euclidean canberra kulczynski jaccard gower altGower morisita horn mountford raup binomial chao cao w -1 c wb r I e t me j sor m -2 co

Value

stat table

Author(s)

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

References

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

See Also

BetaDiv beta_pcoa beta_cpcoa

Examples

# Input otutab, metadata, and options group, method and distance
MicroTest(otu = otutab_rare, map = metadata, group = "Group", Micromet = "MRPP", dist = "bray")
# Input phyloseq format input, and options group, method and distance
MicroTest(ps = ps, group = "Group", Micromet = "MRPP", dist = "bray")

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