funguild_assign: Assign Guilds to Organisms Based on Taxonomic Classification

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Assign Guilds to Organisms Based on Taxonomic Classification

Description

The original function and documentation was written by Brendan Furneaux in the FUNGuildR package.

These functions have identical behavior if supplied with a database; however they download the database corresponding to their name by default.

Taxa present in the database are matched to the taxa present in the supplied otu_table by exact name. In the case of multiple matches, the lowest (most specific) rank is chosen. No attempt is made to check or correct the classification in otu_table$Taxonomy.

Usage

funguild_assign(
  otu_table,
  db_funguild = get_funguild_db(),
  tax_col = "Taxonomy"
)

Arguments

otu_table	A data.frame with a character column named "Taxonomy" (or another name as specified in tax_col), as well as any other columns. Each entry in "otu_table$Taxonomy" should be a comma-, colon-, underscore-, or semicolon-delimited classification of an organism. Rank indicators as given by Sintax ("⁠k:⁠", "⁠p:⁠"...) or Unite ("k__, "p__", ...) are also allowed. A character vector, representing only the taxonomic classification, is also accepted.
db_funguild	A data.frame representing the FUNGuild as returned by get_funguild_db() If not supplied, the default database will be downloaded.
tax_col	A character string, optionally giving an alternate column name in otu_table to use instead of otu_table$Taxonomy.

Value

A tibble::tibble containing all columns of otu_table, plus relevant columns of information from the FUNGuild

Author(s)

Brendan Furneaux (orcid: 0000-0003-3522-7363), modified by Adrien Taudière

References

Nguyen NH, Song Z, Bates ST, Branco S, Tedersoo L, Menke J, Schilling JS, Kennedy PG. 2016. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecology 20:241-248.

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.