betatest: PERMANOVA test for phyloseq

In guokai8/microbial: Do 16s Data Analysis and Generate Figures

Description

PERMANOVA test for phyloseq

Usage

betatest(physeq, group, distance = "bray")

Arguments

physeq	A phyloseq object containing merged information of abundance, taxonomic assignment, sample data including the measured variables and categorical information of the samples, and / or phylogenetic tree if available.
group	(Required). Character string specifying name of a categorical variable that is preferred for grouping the information. information.
distance	A string character specifying dissimilarity index to be used in calculating pairwise distances (Default index is "bray".). "unifrac","wunifrac","manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup" , "binomial", "chao", "cao" or "mahalanobis".

Value

PERMANOVA test result

Author(s)

Kai Guo

Examples

{
data("Physeq")
phy<-normalize(physeq)
beta <-betatest(phy,group="SampleType")
}

guokai8/microbial documentation built on Nov. 10, 2021, 1:43 a.m.