Retrieve gene synonyms from Ensembl

Connects to the Ensembl BioMart database to retrieve gene synonyms for a provided list of gene names. It queries both the 'external_gene_name' and 'external_synonym' filters to maximize match rates.

Usage

gene_synonyms(lookup_genes)

Arguments

lookup_genes

Character vector. A list of gene names (or synonyms) to search for.

Value

A named list where:

• Names are the standard Ensembl external gene names.

• Values are character vectors of unique synonyms for that gene.

Returns NULL if the connection to Ensembl fails or if no genes are found.

Details

The function performs the following steps:

1. Checks if biomaRt is installed.

2. safely connects to the hsapiens_gene_ensembl dataset.

3. Queries Ensembl twice: once matching against gene names and once matching against existing synonyms.

4. Cleans the results by converting empty strings "" to NA and removing incomplete records.

Examples

if (FALSE) { # \dontrun{
  # Basic usage
  syns <- gene_synonyms(c("TP53", "BRCA1"))

  # Access synonyms for TP53
  print(syns$TP53)
} # }