As Phyloseq MicrobiomeR Format

Converts the Taxmap object to the phyloseq_format.

as_phyloseq_format(
  obj,
  otu_table = "otu_abundance",
  tax_data = "otu_annotations",
  sample_data = "sample_data",
  phy_tree = "phy_tree"
)

Arguments

obj

An object to be converted to a Taxmap object with create_taxmap.

otu_table

The name of the observation table with OTU data. Default: NULL

tax_data

The name of the observation table with taxonomic annotations. Default: NULL

sample_data

The name of the observation table with metadata. Default: NULL

phy_tree

The name of the observation data with the phylogenetic tree. Default: NULL

Value

A Taxmap object in the phyloseq_format.

Details

See the MicrobiomeR_Formats documentation.

See also

create_taxmap,order_metacoder_data

Other Formatting: MicrobiomeR_Formats, as_MicrobiomeR_format(), as_analyzed_format(), as_basic_format(), as_custom_format(), as_raw_format(), melt_taxmap(), treatment_matrix()