phyloseq-class: The main experiment-level class for phyloseq data
In phyloseq: Handling and analysis of high-throughput microbiome census data

Description Details See Also

Contains all currently-supported component data classes: otu_table-class, sample_data-class, taxonomyTable-class ("tax_table" slot), phylo-class ("phy_tree" slot), and the XStringSet-class ("refseq" slot). There are several advantages to storing your phylogenetic sequencing experiment as an instance of the phyloseq class, not the least of which is that it is easy to return to the data later and feel confident that the different data types “belong” to one another. Furthermore, the phyloseq constructor ensures that the different data components have compatible indices (e.g. OTUs and samples), and performs the necessary trimming automatically when you create your “experiment-level” object. Downstream analyses are aware of which data classes they require – and where to find them – often making your phyloseq-class object the only data argument required for analysis and plotting functions (although there are many options and parameter arguments available to you).

In the case of missing component data, the slots are set to NULL. As soon as a phyloseq-class object is to be updated with new component data (previously missing/NULL or not), the indices of all components are re-checked for compatibility and trimmed if necessary. This is to ensure by design that components describe the same taxa/samples, and also that these trimming/validity checks do not need to be repeated in downstream analyses.

slots:

otu_table: a single object of class otu_table.
sam_data: a single object of class sample_data.
tax_table: a single object of class taxonomyTable.
phy_tree: a single object of the phylo-class, from the ape package.
refseq: a biological sequence set object of a class that inherits from the XStringSet-class, from the Biostrings package.

The constructor, phyloseq, the merger merge_phyloseq, and also the component constructor/accessors otu_table, sample_data, tax_table, phy_tree, and refseq.