otu_table | R Documentation |
This is the suggested method for both constructing and accessing
Operational Taxonomic Unit (OTU) abundance (otu_table-class
) objects.
When the first
argument is a matrix, otu_table() will attempt to create and return an
otu_table-class object,
which further depends on whether or not taxa_are_rows
is provided as an
additional argument.
Alternatively, if the first argument is an experiment-level (phyloseq-class
)
object, then the corresponding otu_table
is returned.
otu_table(object, taxa_are_rows, errorIfNULL=TRUE) ## S4 method for signature 'phyloseq' otu_table(object, errorIfNULL = TRUE) ## S4 method for signature 'otu_table' otu_table(object, errorIfNULL = TRUE) ## S4 method for signature 'matrix' otu_table(object, taxa_are_rows) ## S4 method for signature 'data.frame' otu_table(object, taxa_are_rows) ## S4 method for signature 'ANY' otu_table(object, errorIfNULL = TRUE)
object |
(Required). An integer matrix, |
taxa_are_rows |
(Conditionally optional). Logical; of length 1. Ignored
unless |
errorIfNULL |
(Optional). Logical. Should the accessor stop with
an error if the slot is empty ( |
An otu_table-class
object.
phy_tree
, sample_data
, tax_table
phyloseq
, merge_phyloseq
# # data(GlobalPatterns) # otu_table(GlobalPatterns)
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