Get gene family assignments for all genes in a PLAZA instance
Usage
get_family_assignments(
instance = c("Dicots", "Monocots", "Diatoms", "Pico"),
type = c("homo", "ortho")
)
Arguments
- instance
Character scalar with name of PLAZA instance for which
gene family assignments will be extracted.
One of 'Dicots', 'Monocots', 'Diatoms', or '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.
- species
Character, species ID.
- gene_id
Character, gene ID.
Examples
fams <- get_family_assignments("Diatoms", type = "ortho")
