Ensembl-to-NCBI gene identifier mappings

Usage

EnsemblToNcbi(object, ...)

# S4 method for class 'EnsemblGenes'
EnsemblToNcbi(object, useCurated = TRUE)

# S4 method for class 'GencodeGenes'
EnsemblToNcbi(object, useCurated = TRUE)

# S4 method for class 'Hgnc'
EnsemblToNcbi(object)

# S4 method for class 'Mgi'
EnsemblToNcbi(object)

# S4 method for class 'character'
EnsemblToNcbi(object, organism = NULL)

Arguments

object: Object.
useCurated: logical(1). Applies to Homo sapiens and Mus musculus only currently. Use current curated mappings from HGNC (human) or MGI (mouse).
organism: character(1). Full Latin organism name (e.g. "Homo sapiens").
...: Additional arguments.

Value

EnsemblToNcbi.

Note

Updated 2023-11-28.

Examples

## character ====
x <- EnsemblToNcbi(
    object = c("ENSG00000000005.6", "ENSG00000000003.16"),
    organism = "Homo sapiens"
)
#> → Matching 2 identifiers against HGNC database.
#> → Importing HGNC complete set.
#> → Caching URL at <https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt> into /private/var/folders/pt/1g5629f1699dfjwdfh32q50m0000gn/T/koopa-r-docs-build-l3dklp41/home/.cache/R/AcidGenomes/BiocFileCache.
#> 
#> → 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(x)
#> Error: object 'x' not found