Get mapping from UniProt IDs to another ID type — getUniProtToIDMapping • einprot

Generate a data.frame with the mapping between UniProtIDs and another ID type. The mapping is obtained from the UniProt ID mapping files (downloaded from https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/).

getUniProtToIDMapping(species, targetId = "Gene_Name")

Arguments

species: Either a taxonomy ID, a species ID or a common species name. See getSupportedSpecies() for valid values.
targetId: Character scalar giving the target ID type. Should be one of the ID types included in the second column in the UniProt ID mapping files. Examples include "Gene_Name", "Ensembl", "STRING", "RefSeq_NT" (depending on the species).

Value

A data.frame with two columns, corresponding to the UniProtID and the corresponding other ID. Note that both columns can have duplicated values, if there is not a one-to-one mapping between UniProtIDs and the other ID type.

Author

Charlotte Soneson

Examples

df <- getUniProtToIDMapping("fission yeast", targetId = "Gene_Name")
head(df)
#>   UniProtID Gene_Name
#> 1    Q9UT08      paa1
#> 2    Q12702      pab1
#> 3    Q10428      par1
#> 4    P78759      par2
#> 5    P78789      amk2
#> 6    Q10343      cbs2