phyloseq: Build phyloseq-class objects from their components.

In phyloseq: Handling and analysis of high-throughput microbiome census data

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))

Example output

[1] TRUE

phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.