map_species {orthogene} | R Documentation |
Search gprofiler
database for species
that match the input text string.
Then translate to a standardised species ID.
map_species( species = NULL, search_cols = c("display_name", "id", "scientific_name", "taxonomy_id"), output_format = c("id", "display_name", "scientific_name", "taxonomy_id", "version"), method = "gprofiler", use_local = TRUE, verbose = TRUE )
species |
Species query
(e.g. "human", "homo sapiens", "hapiens", or 9606).
If given a list, will iterate queries for each item.
Set to |
search_cols |
Which columns to search for
|
output_format |
Which column to return. |
method |
R package to to use for gene mapping:
(slower but more species and genes) or
|
use_local |
If |
verbose |
Print messages. |
Species ID of type output_format
ids <- map_species(species = c( "human", 9606, "mus musculus", "fly", "C elegans" ))