Description Details Author(s) See Also
A S4 Object for storing phyloseq data at all phylogenic levels
This class inherit from the
phyloseq-class
from the phyloseq package. It contains three data classes:
otu_table-class
("otu_table" slot),
sample_data-class
("sample_data" slot), and
taxonomyTable-class
("tax_table" slot).
Besides the three slots inherit from phyloseq-class, the SummarizedPhyloseq
also has 7 more slots, "kingdom_table", "phylum_table", "class_table",
"order_table", "family_table", "genus_table", and "species_table", all in
the class of otu_table-class. This allows you to view the data in different
phylogenic levels.
summarizeFromPhyloseq
is the main constructor for this class, directly from a phyloseq object.
The phyloseq needs to have the otu_table, tax_table, and sample_data to
successfully construct this class.
slots:
a tabular object of the OTU table, class of otu_table-class
a tabular object of the sample meta-data, class of sample_data.
a tabular object of the taxonomy table, class of taxonomyTable.
a tabular object of the summarized OTU table into the kingdom level, class of otu_table
a tabular object of the summarized OTU table into the phylum level, class of otu_table
a tabular object of the summarized OTU table into the class level, class of otu_table
a tabular object of the summarized OTU table into the order level, class of otu_table
a tabular object of the summarized OTU table into the family level, class of otu_table
a tabular object of the summarized OTU table into the genus level, class of otu_table
a tabular object of the summarized OTU table into the species level, class of otu_table
Chenghao Zhu
phyloseq-class
summarizeFromPhyloseq
SummarizedPhyloStats-class
SummarizedPhyloseq-accessors
SummarizedPhyloseq-assign
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