[,otu_table,ANY,ANY,ANY-method {phyloseq} | R Documentation

## Method extensions to extraction operator for phyloseq objects.

### Description

See the documentation for the `Extract` generic, defined in the R `base-package` for the expected behavior.

### Usage

    ## S4 method for signature 'otu_table,ANY,ANY,ANY'
    x[i, j, ..., drop = TRUE]

    ## S4 method for signature 'sample_data,ANY,ANY,ANY'
    x[i, j, ..., drop = TRUE]

    ## S4 method for signature 'taxonomyTable,ANY,ANY,ANY'
    x[i, j, ..., drop = TRUE]

    ## S4 method for signature 'XStringSet,character,ANY,ANY'
    x[i]

### Arguments

`x` | object from which to extract element(s) or in which to replace element(s).
`i` | indices specifying elements to extract or replace. Indices are `numeric` or `character` vectors or empty (missing) or `NULL`. Numeric values are coerced to integer as by `as.integer` (and hence truncated towards zero). Character vectors will be matched to the `names` of the object (or for matrices/arrays, the `dimnames`): see ‘Character indices’ below for further details. For `[`-indexing only: `i`, `j`, `...` can be logical vectors, indicating elements/slices to select. Such vectors are recycled if necessary to match the corresponding extent. `i`, `j`, `...` can also be negative integers, indicating elements/slices to leave out of the selection. When indexing arrays by `[` a single argument `i` can be a matrix with as many columns as there are dimensions of `x`; the result is then a vector with elements corresponding to the sets of indices in each row of `i`. An index value of `NULL` is treated as if it were `integer(0)`.
`j` | See `Extract`
`...` | See `Extract`
`drop` | For matrices and arrays. If `TRUE` the result is coerced to the lowest possible dimension (see the examples). This only works for extracting elements, not for the replacement. See `drop` for further details.

### Details

One special exception to standard behavior of these methods in phyloseq is that the `drop` argument is set internally to `FALSE`. This helps avoid bugs during complicated subsetting with multiple components, where it is necessary to be able to use a two dimensional indexing even if one of those dimensions has only 1 rank. Put another way, these phyloseq-defined extractions never collapse their result into a vector. See the documentation of `Extract` for more information about the `drop` argument.

### See Also

`Extract`

### Examples

    data(esophagus)
    nrow(otu_table(esophagus))
    nrow(otu_table(esophagus)[1:5, ])

[Package phyloseq version 1.24.2 Index]