otu_table {phyloseq} | R Documentation

## Build or access the otu_table.

### Description

This is the suggested method for both constructing and accessing Operational Taxonomic Unit (OTU) abundance (`otu_table-class`) objects. When the first argument is a matrix, otu_table() will attempt to create and return an otu_table-class object, which further depends on whether or not `taxa_are_rows` is provided as an additional argument. Alternatively, if the first argument is an experiment-level (`phyloseq-class`) object, then the corresponding `otu_table` is returned.

### Usage

    otu_table(object, taxa_are_rows, errorIfNULL=TRUE)

    ## S4 method for signature 'phyloseq'
    otu_table(object, errorIfNULL = TRUE)

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

    ## S4 method for signature 'matrix'
    otu_table(object, taxa_are_rows)

    ## S4 method for signature 'data.frame'
    otu_table(object, taxa_are_rows)

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

### Arguments

`object` | (Required). An integer matrix, `otu_table-class`, or `phyloseq-class`.
`taxa_are_rows` | (Conditionally optional). Logical; of length 1. Ignored unless `object` is a matrix, in which case it is is required.
`errorIfNULL` | (Optional). Logical. Should the accessor stop with an error if the slot is empty (`NULL`)? Default `TRUE`. Ignored if `object` argument is a matrix (constructor invoked instead).

### Value

An `otu_table-class` object.

### See Also

`phy_tree`, `sample_data`, `tax_table` `phyloseq`, `merge_phyloseq`

### Examples

    #
    # data(GlobalPatterns)
    # otu_table(GlobalPatterns)

[Package phyloseq version 1.38.0 Index]