Add prokaryote metabolic and ecological functions (FAPROTAX)

Joins the function groups a prokaryotic taxon is known to perform – methanogenesis, denitrification, nitrogen fixation, chitinolysis, human gut association and 87 others – to a taxify() result.

Usage

add_faprotax(x, cols = NULL, verbose = TRUE)

Arguments

x: A data.frame returned by taxify().
cols: Which columns to attach: NULL (default) both, or a character vector of names. See enrichment_cols.
verbose: Logical. Default TRUE.

Value

The same data.frame with faprotax_functions (a |-delimited set) and faprotax_n_functions.

Details

Source: Louca et al. (2016), 92 function groups over 4470 taxa compiled from IJSEM and Bergey's Manual. Redistributed under FAPROTAX's own BSD-style terms; see cite for the notice that must travel with it.

FAPROTAX annotates a taxon at whatever rank the evidence supports, so its entries are a mix of species and genera. The join follows: a species-level entry matches the accepted name, and a taxon with no entry of its own inherits its genus's. Group memberships are the source's; taxifydb reshapes the grouped list into one row per taxon and reduces each entry to the species or genus it names, which the licence requires be stated as a modification.

Functions stay a set rather than one label because a prokaryote genuinely performs several: Escherichia coli carries 17 of them.

References

Louca S, Parfrey LW, Doebeli M (2016) Decoupling function and taxonomy in the global ocean microbiome. Science 353:1272-1277. doi:10.1126/science.aaf4507

Examples

if (FALSE) { # \dontrun{
taxify(c("Escherichia coli", "Nitrosomonas europaea")) |>
  add_faprotax()
} # }