SummarizedPhyloseq-class: S4 class SummarizedPhyloseq

In zhuchcn/phylox: Analyzing and Visualization Microbiome Data on Different Phylogenic Levels

Description

A S4 Object for storing phyloseq data at all phylogenic levels

Details

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:

otu_table

a tabular object of the OTU table, class of otu_table-class

sam_data

a tabular object of the sample meta-data, class of sample_data.

tax_table

a tabular object of the taxonomy table, class of taxonomyTable.

kingdom_table

a tabular object of the summarized OTU table into the kingdom level, class of otu_table

phylum_table

a tabular object of the summarized OTU table into the phylum level, class of otu_table

class_table

a tabular object of the summarized OTU table into the class level, class of otu_table

order_table

a tabular object of the summarized OTU table into the order level, class of otu_table

family_table

a tabular object of the summarized OTU table into the family level, class of otu_table

genus_table

a tabular object of the summarized OTU table into the genus level, class of otu_table

species_table

a tabular object of the summarized OTU table into the species level, class of otu_table

Author(s)

Chenghao Zhu

See Also

phyloseq-class summarizeFromPhyloseq SummarizedPhyloStats-class SummarizedPhyloseq-accessors SummarizedPhyloseq-assign

zhuchcn/phylox documentation built on May 31, 2019, 5:14 p.m.