prune_taxa {phyloseq} | R Documentation

## Prune unwanted OTUs / taxa from a phylogenetic object.

### Description

An S4 Generic method for removing (pruning) unwanted OTUs/taxa from phylogenetic objects, including phylo-class trees, as well as native phyloseq package objects. This is particularly useful for pruning a phyloseq object that has more than one component that describes OTUs. Credit: the `phylo`-class version is adapted from prune.sample.

### Usage

    prune_taxa(taxa, x)

    ## S4 method for signature ''NULL',ANY'
    prune_taxa(taxa, x)

    ## S4 method for signature 'logical,ANY'
    prune_taxa(taxa, x)

    ## S4 method for signature 'character,phylo'
    prune_taxa(taxa, x)

    ## S4 method for signature 'character,otu_table'
    prune_taxa(taxa, x)

    ## S4 method for signature 'character,sample_data'
    prune_taxa(taxa, x)

    ## S4 method for signature 'character,phyloseq'
    prune_taxa(taxa, x)

    ## S4 method for signature 'character,taxonomyTable'
    prune_taxa(taxa, x)

    ## S4 method for signature 'character,XStringSet'
    prune_taxa(taxa, x)

### Arguments

`taxa` | (Required). A character vector of the taxa in object x that you want to keep – OR alternatively – a logical vector where the kept taxa are TRUE, and length is equal to the number of taxa in object x. If `taxa` is a named logical, the taxa retained are based on those names. Make sure they are compatible with the `taxa_names` of the object you are modifying (`x`).
`x` | (Required). A phylogenetic object, including `phylo` trees, as well as all phyloseq classes that represent taxa. If the function `taxa_names` returns a non-`NULL` value, then your object can be pruned by this function.

### Value

The class of the object returned by `prune_taxa` matches the class of the argument, `x`.

### See Also

`prune_samples`

prune.sample

### Examples

    data("esophagus")
    esophagus
    plot(sort(taxa_sums(esophagus), TRUE), type="h", ylim=c(0, 50))
    x1 = prune_taxa(taxa_sums(esophagus) > 10, esophagus)
    x2 = prune_taxa(names(sort(taxa_sums(esophagus), TRUE))[1:9], esophagus)
    identical(x1, x2)

[Package phyloseq version 1.24.2 Index]