subset_samples {phyloseq} | R Documentation

## Subset samples by sample_data expression

### Description

This is a convenience wrapper around the `subset` function. It is intended to allow subsetting complex experimental objects with one function call. Subsetting is based on an expression for which the context first includes the variables contained in `sample_data`. The `samples` retained in the dataset is equivalent to `x[subset & !is.na(subset)]`, where `x` is the vector of sample 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 samples that have a missing value, `NA`, somewhere in the expression.

### Usage

    subset_samples(physeq, ...)

### Arguments

`physeq` | A `sample_data-class`, or a `phyloseq-class` object with a `sample_data`. If the `sample_data` 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 `sample_data`. This is passed on to `subset`, see its documentation for more details.

### Value

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

### See Also

`subset_species`

### Examples

     # data(GlobalPatterns)
     # subset_samples(GlobalPatterns, SampleType=="Ocean")

[Package phyloseq version 1.30.0 Index]