otu_table-methods: Build or access the otu_table.

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

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)

Example output

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