as_phyloseq_format: As Phyloseq MicrobiomeR Format

In vallenderlab/MicrobiomeR: Analyze Microbiome Data

Description

Converts the Taxmap object to the phyloseq_format.

Usage

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

Details

See the MicrobiomeR_Formats documentation.

Value

A Taxmap object in the phyloseq_format.

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

vallenderlab/MicrobiomeR documentation built on Aug. 30, 2019, 11:24 p.m.