ldamarker: Identify biomarker by using LEfSe method

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

Description

Identify biomarker by using LEfSe method

Usage

ldamarker(physeq, group, pvalue = 0.05, normalize = TRUE, method = "relative")

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	group. A character string specifying the name of a categorical variable containing grouping information.
pvalue	pvalue threshold for significant results from kruskal.test
normalize	to normalize the data before analysis(TRUE/FALSE)
method	A list of character strings specifying method to be used to normalize the phyloseq object Available methods are: "relative","TMM","vst","log2".

Author(s)

Kai Guo

Examples

data("Physeq")
res <- ldamarker(physeq,group="group")

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