prune_samples {phyloseq} | R Documentation

## Define a subset of samples to keep in a phyloseq object.

### Description

An S4 Generic method for pruning/filtering unwanted samples by defining those you want to keep.

### Usage

    prune_samples(samples, x)

    ## S4 method for signature 'character,otu_table'
    prune_samples(samples, x)

    ## S4 method for signature 'character,sample_data'
    prune_samples(samples, x)

    ## S4 method for signature 'character,phyloseq'
    prune_samples(samples, x)

    ## S4 method for signature 'logical,ANY'
    prune_samples(samples, x)

### Arguments

`samples` | (Required). A character vector of the samples in object x that you want to keep – OR alternatively – a logical vector where the kept samples are TRUE, and length is equal to the number of samples in object x. If `samples` is a named logical, the samples retained is based on those names. Make sure they are compatible with the `sample_names` of the object you are modifying (`x`).
`x` | A phyloseq object.

### Value

The class of the object returned by `prune_samples` matches the class of the phyloseq object, `x`.

### See Also

`subset_samples`

### Examples

     data(GlobalPatterns)
     # Subset to just the Chlamydiae phylum.
     GP.chl <- subset_taxa(GlobalPatterns, Phylum=="Chlamydiae")
     # Remove the samples that have less than 20 total reads from Chlamydiae
     GP.chl <- prune_samples(sample_sums(GP.chl)>=20, GP.chl)
     # (p <- plot_tree(GP.chl, color="SampleType", shape="Family", label.tips="Genus", size="abundance"))

[Package phyloseq version 1.24.2 Index]