Map protein identifiers to genes

Usage

makeProteinToGeneFromEnsembl(
  ids,
  organism = NULL,
  genomeBuild = NULL,
  release = NULL
)

Arguments

ids: character. Ensembl protein identifiers. Human proteins are prefixed with "ENSP", for example.
organism: character(1). Full Latin organism name (e.g. "Homo sapiens").
genomeBuild: character(1). Ensembl genome build assembly name (e.g. "GRCh38"). If set NULL, defaults to the most recent build available. Note: don't pass in UCSC build IDs (e.g. "hg38").
release: integer(1). Ensembl release version (e.g. 100). We recommend setting this value if possible, for improved reproducibility. When left unset, the latest release available via AnnotationHub/ensembldb is used. Note that the latest version available can vary, depending on the versions of AnnotationHub and ensembldb in use.

Value

ProteinToGene.

Note

Updated 2023-09-16.

Examples

ids <- c("ENSP00000238714", "ENSP00000338157")
object <- makeProteinToGeneFromEnsembl(ids)
#> → Making <ProteinToGene> from Ensembl.
#> → Getting <EnsDb> from AnnotationHub 3.10.0 (2023-10-20).
#> ℹ "AH113665": Ensembl 110 EnsDb for Homo sapiens.
#> Organism: Homo sapiens
#> Genome build: GRCh38
#> Release: 110
print(object)
#> ProteinToGene with 2 rows and 3 columns
#>         proteinId          geneId    geneName
#>       <character>     <character> <character>
#> 1 ENSP00000238714 ENSG00000115421      PAPOLG
#> 2 ENSP00000338157 ENSG00000109906      ZBTB16