phyloseq: get_sample-methods – R documentation

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get_sample-methods

Returns all abundance values for species i.

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

get_sample(physeq, i)

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

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

`physeq`	(Required). `otu_table-class`, or `phyloseq-class`.
`i`	(Required). A single taxa/species/OTU ID for which you want to know the abundance in each sample.

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

data(esophagus)
taxa_names(esophagus)
get_sample(esophagus, "59_5_19")

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