access {phyloseq} | R Documentation

## Universal slot accessor function for phyloseq-class.

### Description

This function is used internally by many accessors and in many functions/methods that need to access a particular type of component data. If something is wrong, or the slot is missing, the expected behavior is that this function will return NULL. Thus, the output can be tested by `is.null` as verification of the presence of a particular data component. Unlike the component-specific accessors (e.g. `otu_table`, or `phy_tree`), the default behavior is not to stop with an error if the desired slot is empty. In all cases this is controlled by the `errorIfNULL` argument, which can be set to `TRUE` if an error is desired.

### Usage

    access(physeq, slot, errorIfNULL=FALSE)

### Arguments

`physeq` | (Required). `phyloseq-class`.
`slot` | (Required). A character string indicating the slot (not data class) of the component data type that is desired.
`errorIfNULL` | (Optional). Logical. Should the accessor stop with an error if the slot is empty (`NULL`)? Default `FALSE`.

### Value

Returns the component object specified by the argument `slot`. Returns NULL if slot does not exist. Returns `physeq` as-is if it is a component class that already matches the slot name.

### See Also

`getslots.phyloseq`, `merge_phyloseq`

### Examples

    #
    ## data(GlobalPatterns)
    ## access(GlobalPatterns, "tax_table")
    ## access(GlobalPatterns, "phy_tree")
    ## access(otu_table(GlobalPatterns), "otu_table")
    ## # Should return NULL:
    ## access(otu_table(GlobalPatterns), "sample_data")
    ## access(otuTree(GlobalPatterns), "sample_data")
    ## access(otuSam(GlobalPatterns), "phy_tree")

[Package phyloseq version 1.28.0 Index]