Map protein identifiers to genes

makeProtein2GeneFromEnsembl(
  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. 90). 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

Protein2Gene.

Note

Updated 2021-02-01.

Examples

ids <- c("ENSP00000238714", "ENSP00000338157") makeProtein2GeneFromEnsembl(ids)
#> → Making `Protein2Gene` from Ensembl.
#> → Getting `EnsDb` from AnnotationHub 2.22.0 (2020-10-27).
#> AH89426: Ensembl 103 EnsDb for Homo sapiens.
#> Organism: Homo sapiens
#> Genome build: GRCh38
#> Release: 103
#> Protein2Gene with 2 rows and 3 columns #> proteinId geneId geneName #> <character> <character> <character> #> 1 ENSP00000238714 ENSG00000115421 PAPOLG #> 2 ENSP00000338157 ENSG00000109906 ZBTB16