Update gene symbols — updateGeneSymbols • AcidGenomes

Update gene symbols

Usage

updateGeneSymbols(geneNames, organism)

Arguments

geneNames: character. Gene names (symbols).
organism: character(1). Full Latin organism name (e.g. "Homo sapiens").

Value

character. Named character, with original input defined in the names.

Details

Human genes are checked against HGNC. Other organisms are checked against NCBI.

Intentionally errors on match failure.

Note

Updated 2023-12-21.

See also

https://twitter.com/samuel_marsh/status/1737855289876201922
https://waldronlab.io/HGNChelper/

Examples

## Homo sapiens ====
object <- updateGeneSymbols(
    geneNames = c("ZCCHC6", "ZCCHC11"),
    organism = "Homo sapiens"
)
#> → Importing HGNC complete set.
#> Error in vapply(X = X, FUN = FUN, FUN.VALUE = logical(1L), ..., USE.NAMES = useNames): formal argument "USE.NAMES" matched by multiple actual arguments
print(object)
#> Error: object 'object' not found

## Mus musculus ====
object <- updateGeneSymbols(
    geneNames = c("Zcchc6", "Zcchc11"),
    organism = "Mus musculus"
)
#> → Downloading Mus musculus gene info from NCBI at <https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz>.
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'con' in selecting a method for function 'import': formal argument "USE.NAMES" matched by multiple actual arguments
print(object)
#> Error: object 'object' not found