abundances {microbiomeMarker} | R Documentation |
Extract taxa abundances from phyloseq objects.
abundances(object, transform = c("identity", "log10", "log10p"), norm = FALSE) ## S4 method for signature 'otu_table' abundances(object, transform = c("identity", "log10", "log10p"), norm = FALSE) ## S4 method for signature 'phyloseq' abundances(object, transform = c("identity", "log10", "log10p"), norm = FALSE) ## S4 method for signature 'microbiomeMarker' abundances(object, transform = c("identity", "log10", "log10p"))
object |
|
transform |
transformation to apply, the options inclulde:
|
norm |
logical, indicating whether or not to return the normalized taxa abundances. |
abundance matrix with taxa in rows and samples in columns.
otu_table
, phyloseq
,
microbiomeMarker
,transform_abundances
data(caporaso) abd <- abundances(caporaso)