phyloseq {phyloseq} | R Documentation

## 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))

[Package phyloseq version 1.32.0 Index]