access: Universal slot accessor function for phyloseq-class.

In phyloseq: Handling and analysis of high-throughput microbiome census data

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")

Example output

phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.