phyloseq: refseq-methods – R documentation

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refseq-methods

Retrieve reference sequences (XStringSet-class) from object.

Description

This is the suggested method for accessing the phylogenetic tree, (XStringSet-class) from a phyloseq data object (phyloseq-class). Like other accessors (see See Also, below), the default behavior of this method is to stop with an error if physeq is a phyloseq-class but does not contain reference sequences (the component data type you are trying to access in this case).

Usage

refseq(physeq, errorIfNULL=TRUE)

## S4 method for signature 'ANY'
refseq(physeq, errorIfNULL = TRUE)

## S4 method for signature 'XStringSet'
refseq(physeq)

Arguments

`physeq`	(Required). An instance of phyloseq-class that contains a phylogenetic tree. If physeq is a phylogenetic tree (a component data class), then it is returned as-is.
`errorIfNULL`	(Optional). Logical. Should the accessor stop with an error if the slot is empty (`NULL`)? Default `TRUE`.

Value

The phylo-class object contained within physeq; or NULL if physeq does not have a tree. This method stops with an error in the latter NULL case be default, which can be over-ridden by changing the value of errorIfNULL to FALSE.

Examples

data(GlobalPatterns)
 refseq(GlobalPatterns, FALSE)

phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23