tax_table<- {phyloseq} | R Documentation

## Assign a (new) Taxonomy Table to `x`

### Description

Assign a (new) Taxonomy Table to `x`

### Usage

    tax_table(x) <- value

    ## S4 replacement method for signature 'phyloseq,taxonomyTable'
    tax_table(x) <- value

    ## S4 replacement method for signature 'phyloseq,ANY'
    tax_table(x) <- value

    ## S4 replacement method for signature 'taxonomyTable,taxonomyTable'
    tax_table(x) <- value

    ## S4 replacement method for signature 'taxonomyTable,ANY'
    tax_table(x) <- value

### Arguments

`x` | (Required). `phyloseq-class`
`value` | (Required). `taxonomyTable-class`. Alternatively, `value` can be a `phyloseq-class` that has a `tax_table` component, or a `matrix-class` that can be coerced to a `taxonomyTable-class` with row indices that match at least some of the `taxa_names` of `x`.

### Examples

    # data(GlobalPatterns)
    # # An example of pruning to just the first 100 taxa in GlobalPatterns.
    # ex2a <- prune_taxa(taxa_names(GlobalPatterns)[1:100], GlobalPatterns)
    # # The following 3 lines produces an ex2b that is equal to ex2a
    # ex2b <- GlobalPatterns
    # TT <- tax_table(GlobalPatterns)[1:100, ]
    # tax_table(ex2b) <- TT
    # identical(ex2a, ex2b)
    # print(ex2b)
    # # 2 examples adding a tax_table component from phyloseq or matrix classes
    # ex2c <- phyloseq(otu_table(ex2b), sample_data(ex2b), phy_tree(ex2b))
    # tax_table(ex2c) <- ex2b
    # identical(ex2a, ex2c)
    # ex2c <- phyloseq(otu_table(ex2b), sample_data(ex2b), phy_tree(ex2b))
    # tax_table(ex2c) <- as(tax_table(ex2b), "matrix")
    # identical(ex2a, ex2c)

[Package phyloseq version 1.24.2 Index]