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.