Get enriched functional terms in gene families of a PLAZA instance — get_family_functions • rplaza

Get enriched functional terms in gene families of a PLAZA instance

Usage

get_family_functions(
  instance = c("Dicots", "Monocots"),
  type = c("homo", "ortho")
)

Arguments

instance: Character scalar with name of PLAZA instance for which gene family functions will be extracted. One of 'Dicots' or 'Monocots' (not available for 'Diatoms' and 'Pico').
type: Character indicating the type of gene family to use. One of 'homo' (homologous gene families) or 'ortho' (orthologous gene families).

Value

A data frame (or list of data frames, in case of multiple species) with the following variables:

family_id: Character, gene family ID.
term_id: Character, functional term ID.
term_description: Character, functional term description.
ontology: Character, ontology from where term comes.
score: Numeric, enrichment score.

Examples

fam_func <- get_family_functions("Dicots", type = "ortho")