Retrieve reference sequences (XStringSet-class) from object.
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).
refseq(physeq, errorIfNULL=TRUE) ## S4 method for signature 'ANY' refseq(physeq, errorIfNULL = TRUE) ## S4 method for signature 'XStringSet' refseq(physeq)
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 ( |
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
.
data(GlobalPatterns) refseq(GlobalPatterns, FALSE)
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