normalize: Normalize the phyloseq object with different methods

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

Normalize the phyloseq object with different methods

Description

Normalize the phyloseq object with different methods

Usage

normalize(physeq, group, method = "relative", table = FALSE)

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 (DESeq2). A character string specifying the name of a categorical variable containing grouping information.
method	A list of character strings specifying method to be used to normalize the phyloseq object Available methods are: "relative","TMM","vst","log2".
table	return a data.frame or not

Value

phyloseq object with normalized data

Author(s)

Kai Guo

Examples

{
data("Physeq")
phy<-normalize(physeq)
}

guokai8/microbial documentation built on Oct. 15, 2024, 11:32 p.m.