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Get rank information for a taxonomy format

Source: R/utils.R
tax_prefixes.Rd

lifecycle-experimental

Returns the taxonomic rank information for common reference database formats. For prefix-based formats (unite, sintax, greengenes2), returns a named character vector of prefixes. For positional formats (pr2), returns a named integer vector of rank positions.

Use the result with list_ranks_db() and summarize_db() via their tax_format parameter.

Note: dada2::assignTaxonomy() is a classifier, not a taxonomy format. It accepts any semicolon-separated taxonomy with any number of levels, regardless of whether prefixes are present or not. Use the taxLevels argument in dada2::assignTaxonomy() to specify the rank names.

Usage

tax_prefixes(tax_format = c("unite", "sintax", "greengenes2", "pr2"))

Arguments

tax_format

(Character) One of:

  • "unite": k__/p__/... format used by UNITE general FASTA releases.

  • "sintax": d:/k:/p:/... format used by VSEARCH SINTAX and USEARCH UTAX databases (UNITE SINTAX, PR2 UTAX). Note that UNITE SINTAX files use k: (kingdom) as their first rank and do not include d: (domain). When calling summarize_db() on a UNITE SINTAX file, the d: row will show 0 sequences — this is expected.

  • "greengenes2": d__/p__/... format used by Greengenes2 (starts with domain d__ instead of kingdom k__).

  • "pr2": positional format with 9 levels specific to protist taxonomy: Domain, Supergroup, Division, Subdivision, Class, Order, Family, Genus, Species.

Value

For prefix-based formats: a named character vector of rank prefixes. For positional formats: a named integer vector of rank positions.

See also

list_ranks_db(), summarize_db(), detect_tax_format()

Examples

tax_prefixes("unite")
#>     k     p     c     o     f     g     s 
#> "k__" "p__" "c__" "o__" "f__" "g__" "s__" 
tax_prefixes("sintax")
#>    d    k    p    c    o    f    g    s 
#> "d:" "k:" "p:" "c:" "o:" "f:" "g:" "s:" 
tax_prefixes("greengenes2")
#>     d     p     c     o     f     g     s 
#> "d__" "p__" "c__" "o__" "f__" "g__" "s__" 
tax_prefixes("pr2")
#>      Domain  Supergroup    Division Subdivision       Class       Order 
#>           1           2           3           4           5           6 
#>      Family       Genus     Species 
#>           7           8           9