SIPmg (version 3.0)

tax.table: phyloseq taxa table from GTDB taxonomy input

Description

A MAG table, similar to OTU table in phyloseq, will be generated from a concantenated GTDB taxa table for bacteria and archaea

Usage

tax.table(taxonomy)

Value

phyloseq-style taxonomy table, but for MAGs

Arguments

taxonomy

GTDB taxonomy data frame. A taxonomy file in the GTDB output format. Load the bacteria and archaea taxonomy outputs separately. The markdown requires loading the standard output files from GTDB-Tk separately for bacteria and archaea

Examples

data(taxonomy_tibble)

# \donttest{

### Making phyloseq table from taxonomy metadata
taxonomy.object = tax.table(taxonomy_tibble)
# }