phyloseq: get_taxa-methods – R documentation

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get_taxa-methods

Returns all abundance values of sample i.

This is a simple accessor function for investigating a single sample-of-interest.

get_taxa(physeq, i)

## S4 method for signature 'otu_table'
get_taxa(physeq, i)

## S4 method for signature 'phyloseq'
get_taxa(physeq, i)

`physeq`	(Required). `otu_table-class`, or `phyloseq-class`.
`i`	(Required). A single sample for which you want to know the abundance of each species. Can be integer for index value, or sample name.

An integer vector of the abundance values for each species in physeq for sample i

data(esophagus)
sample_names(esophagus)
get_taxa(esophagus, "B")

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