hgnc_lookuptable: Parse HGNC gene identifier lookup table that was downloaded...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Parse HGNC gene identifier lookup table that was downloaded from genenames.org

Description

download link: https://www.genenames.org/download/statistics-and-files/ table: "Complete dataset download links" –>> "Complete HGNC approved dataset text json" –>> download the "TXT" table filename is typically something like hgnc_complete_set.txt URL as of September 2023; https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt

Usage

hgnc_lookuptable(f, uppercase_symbols = TRUE)

Arguments

f	full path to the downloaded table (expected to be tsv format)
uppercase_symbols	convert all gene symbols to upper case? default: TRUE

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

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.