microbial (version 0.0.19)

ldamarker: Identify biomarker by using LEfSe method

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".

Examples

# NOT RUN {
data("Physeq")
res <- ldamarker(physeq,group="group")
# }
# NOT RUN {
# }