Download gene annotation reference table from Ensembl — download_gene

Downloads a standardized gene annotation table for human or mouse using biomaRt. Includes Ensembl ID, gene symbol, Entrez ID, gene type, chromosome location, and other metadata.

Usage

download_gene_ref(
  species = c("human", "mouse"),
  remove_empty_symbol = FALSE,
  remove_na_entrez = FALSE,
  save = FALSE,
  save_path = NULL
)

Arguments

species: Organism, either "human" or "mouse". Default is "human".
remove_empty_symbol: Logical. Remove entries with missing gene symbol. Default: FALSE.
remove_na_entrez: Logical. Remove entries with missing Entrez ID. Default: FALSE.
save: Logical. Whether to save the result as .rds. Default: FALSE.
save_path: File path to save (optional). If NULL, will use default gene_ref_<species>_<date>.rds.

Value

A data.frame containing gene annotation.