microbial (version 0.0.19)

normalize: 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

Examples

# NOT RUN {
{
data("Physeq")
phy<-normalize(physeq)
}
# }