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:
phylo-class, from the ape
package.XStringSet-class, from the
Biostrings package.phyloseq, the merger
merge_phyloseq, and also the component
constructor/accessors otu_table,
sample_data, tax_table,
phy_tree, and refseq.