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