All species

Source: R/all_species.R

List all species currently supported by orthogene. Wrapper function for map_species. When method=NULL, all species from all available methods will be returned.

all_species(method = NULL, verbose = TRUE)

Arguments

method

R package to use for gene mapping:

  • "gprofiler" : Slower but more species and genes.

  • "homologene" : Faster but fewer species and genes.

  • "babelgene" : Faster but fewer species and genes. Also gives consensus scores for each gene mapping based on a several different data sources.

verbose

Print messages.

Value

data.table of species names, provided in multiple formats.

Examples

species_dt <- all_species()
#> Retrieving all organisms available in homologene.
#> Returning table with all species.
#> Retrieving all organisms available in gprofiler.
#> Using stored `gprofiler_orgs`.
#> Returning table with all species.
#> Retrieving all organisms available in babelgene.
#> Returning table with all species.