A S4 class extending phyloseq for microbiome data analysis

This class inherits from phyloseq and adds a slot for additional information, such as lowest taxonomic rank, MetaPhlAn database version, applied transformations and/or filters.

show() displays a summary of a microEDA object, including the standard phyloseq output and information from the info slot.

Usage

microEDA(tax_profile, metadata = NULL, sample_column = NULL)

# S4 method for class 'metaphlanProfile'
microEDA(tax_profile, metadata = NULL, sample_column = NULL)

# S4 method for class 'phyloseq'
microEDA(tax_profile, metadata = NULL, sample_column = NULL)

# S4 method for class 'microEDA'
show(object)

Arguments

tax_profile: An object of class metaphlanProfile or phyloseq.
metadata: Optional data.frame with sample metadata.
sample_column: Character string specifying the column name in metadata that contains sample identifiers (e.g., "Samples").
object: A microEDA object.

Value

An object of class microEDA.

Details

When passed a metaphlanProfile, the profile will be returned at the lowest available taxonomic rank, which usually is at strain rank. To agglomerate the profile at a higher rank, please see agglomerate_taxa().

Slots

info: A list containing metadata.
otu_table: A matrix of class otu_table with taxa as rows and samples as columns.
tax_table: A named character matrix of class taxonomyTable, with taxon IDs as row names and taxonomic ranks as columns.
sam_data: An object of class sample_data containing sample metadata.
phy_tree: An object of class phylo representing a phylogenetic tree.
refseq: An object of a class inheriting from XStringSet-class (e.g., DNAStringSet) containing biological sequences. See XStringSet.

Examples

data("GlobalPatterns", package = "phyloseq")
me <- microEDA(GlobalPatterns)