Look up gene coordinates from Ensembl via biomaRt — get_gene

Queries Ensembl for genomic coordinates of one or more HGNC gene symbols. Results are filtered to standard chromosomes (1–22, X, Y), deduplicated (widest range per gene, preferring autosomes), and returned as a tibble.

Usage

get_gene_coords(genes, build = c("grch38", "grch37"))

Arguments

genes: Character vector of HGNC gene symbols.
build: Genome build: "grch38" (default) or "grch37".

Value

A tibble with columns hgnc_symbol, chromosome, start, end. Genes not found in Ensembl are dropped with a warning.

Examples

get_gene_coords("CD40")
#> Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery,     quote = quote, numAttributes = length(attributes)): Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
get_gene_coords(c("CD40", "APOE"), build = "grch37")
#> Error in req_perform(request): HTTP 504 Gateway Timeout.