phyloseq: sample_data-methods – R documentation

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sample_data-methods

Build or access sample_data.

Description

This is the suggested method for both constructing and accessing a table of sample-level variables (sample_data-class), which in the phyloseq-package is represented as a special extension of the data.frame-class. When the argument is a data.frame, sample_data will create a sample_data-class object. In this case, the rows should be named to match the sample_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 sample_data 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 sample_data.

Usage

sample_data(object, errorIfNULL=TRUE)

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

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

Arguments

`object`	(Required). A `data.frame-class`, or a `phyloseq-class` object.
`errorIfNULL`	(Optional). Logical. Should the accessor stop with an error if the slot is empty (`NULL`)? Default `TRUE`.

Value

A sample_data-class object representing the sample variates of an experiment.

Examples

#
data(soilrep)
head(sample_data(soilrep))

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