phyloseq (version 1.16.2)

refseq: 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)
## S3 method for class 'ANY':
refseq(physeq, errorIfNULL = TRUE)
## S3 method for class '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.

See Also

otu_table, sample_data, tax_table phy_tree, phyloseq, merge_phyloseq

Examples

data(GlobalPatterns)
 refseq(GlobalPatterns, FALSE)