hgnc_idmap_table {goat}

Parse HGNC gene identifier lookup table that was downloaded from genenames.org into a table with HGNC ID, symbol, synonym (NA if unavailable), entrez ID

Description

download link: https://www.genenames.org/download/statistics-and-files/ table: "Complete dataset download links" –>> "Complete HGNC approved dataset" –>> download the "TXT" table filename is typically something like hgnc_complete_set.txt URL; https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt

Usage

hgnc_idmap_table(filename)

Arguments

filename

full path to the downloaded table (expected to be tsv format, typically has .txt or .tsv file extension)

Value

a long-format table with columns; hgnc_id, hgnc_symbol, type, value

alternatively;

table: "Total Approved Symbols" –>> "TXT" / "text file in TSV format" filename is typically something like non_alt_loci_set.txt