Read community data written by tidytacos

read_tidytacos() reads the three .csv files created by the write_tidytacos() function and returns a tidytacos object.

Usage

read_tidytacos(
  din,
  samples = "samples.csv",
  taxa = "taxa.csv",
  counts = "counts.csv"
)

Arguments

din

directory containing the sample, taxa and counts table in csv format

samples

the name of the samples table, defaults to samples.csv

taxa

the name of the taxa table, defaults to taxa.csv

counts

the name of the counts table, defaults to counts.csv

Value

A tidytacos object.

Details

The samples.csv file should contain a column named "sample_id". The taxa.csv file should contain a column named "taxon_id" and at the very least one rank name. The default rank names used by tidytacos are "domain", "phylum", "class", "order", "family", "genus" and "species". The counts.csv file should contain columns named "sample_id", "taxon_id" and "count".

See also

Other import-methods: create_tidytacos(), from_dada(), from_phyloseq()