Extract taxa abundances

Source: R/abundances-methods.R

Extract taxa abundances from phyloseq objects.

abundances(object, transform = c("identity", "log10", "log10p"), norm = FALSE)

# S4 method for otu_table
abundances(object, transform = c("identity", "log10", "log10p"), norm = FALSE)

# S4 method for phyloseq
abundances(object, transform = c("identity", "log10", "log10p"), norm = FALSE)

# S4 method for microbiomeMarker
abundances(object, transform = c("identity", "log10", "log10p"))

Arguments

object

otu_table, phyloseq, or microbiomeMarker.

transform

transformation to apply, the options inclulde:

  • "identity", return the original data without any transformation.

  • "log10", the transformation is log10(object), and if the data contains zeros the transformation is log10(1 + object).

  • "log10p", the transformation is log10(1 + object).

norm

logical, indicating whether or not to return the normalized taxa abundances.

Value

abundance matrix with taxa in rows and samples in columns.

See also

otu_table, phyloseq, microbiomeMarker,transform_abundances

Examples

data(caporaso)
abd <- abundances(caporaso)