subset_taxa {phyloseq} | R Documentation

## Subset species by taxonomic expression

### Description

This is a convenience wrapper around the `subset` function. It is intended to speed subsetting complex experimental objects with one function call. In the case of `subset_taxa`, the subsetting will be based on an expression related to the columns and values within the `tax_table` (`taxonomyTable` component) slot of `physeq`. The `OTUs` retained in the dataset is equivalent to `x[subset & !is.na(subset)]`, where `x` is the vector of OTU IDs and `subset` is the logical that results from your subsetting expression. This is important to keep in mind, as users are often unaware that this subsetting step also removes/omits OTUs that have a missing value result, `NA`, somewhere in the expression.

### Usage

    subset_taxa(physeq, ...)

### Arguments

`physeq` | A `taxonomyTable-class`, or `phyloseq-class` that contains a taxonomyTable. If the `tax_table` slot is missing in `physeq`, then `physeq` will be returned as-is and a warning will be printed to screen.
`...` | The subsetting expression that should be applied to the `taxonomyTable`. This is passed on to `subset`, and more details and examples about how it functions can be found in its documentation.

### Value

A subsetted object with the same class as `physeq`.

### See Also

`subset_samples`

### Examples

    ## ex3 <- subset_taxa(GlobalPatterns, Phylum=="Bacteroidetes")

[Package phyloseq version 1.34.0 Index]