Skip to contents

This function checks and updates gene symbols in a matrix's row names to ensure they conform to the current approved HGNC (HUGO Gene Nomenclature Committee) standards. Non-standard or outdated gene symbols are replaced with their current official symbols.

Usage

update_gene_symbols(data, verbose = FALSE)

Arguments

data

A numeric matrix containing gene expression or protein abundance data with gene identifiers as row names.

verbose

A logical value indicating whether to print detailed messages about the number of approved, non-approved, and unmappable gene symbols. Default is FALSE.

Value

A matrix with updated gene symbols as row names. Rows with unmappable symbols (where no suggested symbol could be found) are removed from the output.

Details

The function uses the HGNChelper package to check and standardize gene symbols based on a predefined gene symbols map. This is important for ensuring consistency in gene naming across datasets and avoiding issues with outdated or non-standard gene symbols.