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.
#> → Importing /private/var/folders/pt/1g5629f1699dfjwdfh32q50m0000gn/T/koopa-r-docs-build-l3dklp41/home/.cache/R/AcidGenomes/BiocFileCache/a36529a1d43e_hgnc_complete_set.txt using base::`read.table()`.
#> Error in stop(simpleError(message = msg, call = if (p) {    sys.call(p)})): Assert failure.
#> [1] areSetEqual(names(expected), names(object)) is not TRUE.
#> Cause: `character` and `character` have different numbers of elements (52
#> versus 51).
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>.
#> → Importing /private/var/folders/pt/1g5629f1699dfjwdfh32q50m0000gn/T/koopa-r-docs-build-l3dklp41/home/.cache/R/AcidGenomes/BiocFileCache/a36560c5e72_Mus_musculus.gene_info.gz using base::`read.table()`.
print(object)
#>  Zcchc6 Zcchc11 
#>  "Tut7"  "Tut4"