Description Usage Arguments Details Value See Also Examples
View source: R/transform_filter-methods.R
All tips of the tree separated by a cophenetic distance smaller than
h
will be agglomerated into one taxa using merge_taxa
.
1 |
physeq |
(Required). A |
h |
(Optional). Numeric scalar of the height where the tree should be cut.
This refers to the tree resulting from hierarchical clustering
of |
hcfun |
(Optional). A function.
The (agglomerative, hierarchical) clustering function to use.
Good examples are
|
... |
(Optional). Additional named arguments to pass
to |
Can be used to create a non-trivial OTU Table, if a phylogenetic tree is available.
For now, a simple, “greedy”, single-linkage clustering is used. In future releases
it should be possible to specify different clustering approaches available in R
,
in particular, complete-linkage clustering appears to be used more commonly for OTU
clustering applications.
An instance of the phyloseq-class
.
Or alternatively, a phylo
object if the
physeq
argument was just a tree.
In the expected-use case, the number of OTUs will be fewer
(see ntaxa
),
after merging OTUs that are related enough to be called
the same OTU.
1 2 3 4 5 |
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