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 Non-standard or outdated gene symbols are replaced with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with outdated or non-standard gene symbols.