phyloseq (version 1.16.2)

phyloseq: Build phyloseq-class objects from their components.

Description

phyloseq() is a constructor method, This is the main method suggested for constructing an experiment-level (phyloseq-class) object from its component data (component data classes: otu_table-class, sample_data-class, taxonomyTable-class, phylo-class).

Usage

phyloseq(...)

Arguments

...

One or more component objects among the set of classes defined by the phyloseq package, as well as phylo-class (defined by the ape-package). Each argument should be a different class. For combining multiple components of the same class, or multiple phyloseq-class objects, use the merge_phyloseq function. Unlike in earlier versions, the arguments to phyloseq do not need to be named, and the order of the arguments does not matter.

Value

• The class of the returned object depends on the argument class(es). For an experiment-level object, two or more component data objects must be provided. Otherwise, if a single component-class is provided, it is simply returned as-is. The order of arguments does not matter.

See Also

merge_phyloseq

Examples

data(esophagus)
x1 = phyloseq(otu_table(esophagus), phy_tree(esophagus))
identical(x1, esophagus)
# # data(GlobalPatterns)
# # GP <- GlobalPatterns
# # phyloseq(sample_data(GP), otu_table(GP))
# # phyloseq(otu_table(GP), phy_tree(GP))
# # phyloseq(tax_table(GP), otu_table(GP))
# # phyloseq(phy_tree(GP), otu_table(GP), sample_data(GP))
# # phyloseq(otu_table(GP), tax_table(GP), sample_data(GP))
# # phyloseq(otu_table(GP), phy_tree(GP), tax_table(GP), sample_data(GP))