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).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: [object Object],[object Object],[object Object],[object Object],[object Object]
phyloseq,
the merger merge_phyloseq, and also the component
constructor/accessors otu_table, sample_data,
tax_table, phy_tree, and refseq.