phyloseq: otu_table-methods – R documentation

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otu_table-methods

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.

Examples

#
# data(GlobalPatterns)
# otu_table(GlobalPatterns)

phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23