tax_table {phyloseq} | R Documentation

## Build or access the taxonomyTable.

### Description

This is the suggested method for both constructing and accessing a table of taxonomic names, organized with ranks as columns (`taxonomyTable-class`). When the argument is a character matrix, tax_table() will create and return a `taxonomyTable-class` object. In this case, the rows should be named to match the `species.names` of the other objects to which it will ultimately be paired. Alternatively, if the first argument is an experiment-level (`phyloseq-class`) object, then the corresponding `taxonomyTable` is returned. Like other accessors (see See Also, below), the default behavior of this method is to stop with an error if `object` is a `phyloseq-class` but does not contain a `taxonomyTable`.

### Usage

    tax_table(object, errorIfNULL=TRUE)

    ## S4 method for signature 'ANY'
    tax_table(object, errorIfNULL = TRUE)

    ## S4 method for signature 'matrix'
    tax_table(object)

    ## S4 method for signature 'data.frame'
    tax_table(object)

### Arguments

`object` | An object among the set of classes defined by the phyloseq package that contain taxonomyTable.
`errorIfNULL` | (Optional). Logical. Should the accessor stop with an error if the slot is empty (`NULL`)? Default `TRUE`.

### Value

A `taxonomyTable-class` object. It is either grabbed from the relevant slot if `object` is complex, or built anew if `object` is a character matrix representing the taxonomic classification of species in the experiment.

### See Also

`phy_tree`, `sample_data`, `otu_table` `phyloseq`, `merge_phyloseq`

### Examples

    #
    # tax1 <- tax_table(matrix("abc", 30, 8))
    # data(GlobalPatterns)
    # tax_table(GlobalPatterns)

[Package phyloseq version 1.26.1 Index]