Build or access the taxonomyTable.
This is the suggested method for both constructing and accessing a table of
taxonomic names, organized with ranks as columns (taxonomyTable-class).
When the argument is a character matrix, tax_table() will create and return a
taxonomyTable-class object.
In this case, the rows should be named to match the
species.names of the other objects to which it will ultimately be paired.
Alternatively, if the first argument is an experiment-level (phyloseq-class)
object, then the corresponding taxonomyTable is returned.
Like other accessors (see See Also, below), the default behavior of this method
is to stop with an
error if object is a phyloseq-class but does not
contain a taxonomyTable.
tax_table(object, errorIfNULL=TRUE) ## S4 method for signature 'ANY' tax_table(object, errorIfNULL = TRUE) ## S4 method for signature 'matrix' tax_table(object) ## S4 method for signature 'data.frame' tax_table(object)
object |
An object among the set of classes defined by the phyloseq package that contain taxonomyTable. |
errorIfNULL |
(Optional). Logical. Should the accessor stop with
an error if the slot is empty ( |
A taxonomyTable-class object.
It is either grabbed from the relevant slot
if object is complex, or built anew if object is a
character matrix representing the taxonomic classification of
species in the experiment.
#
# tax1 <- tax_table(matrix("abc", 30, 8))
# data(GlobalPatterns)
# tax_table(GlobalPatterns)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.