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Creates an ID translation table from UniProt data

Source: R/id_mapping.R
uniprot_full_id_mapping_table.Rd

Creates an ID translation table from UniProt data

Usage

uniprot_full_id_mapping_table(
  to,
  from = "accession",
  reviewed = TRUE,
  organism = 9606
)

Arguments

to

Character or symbol: target ID type. See Details for possible values.

from

Character or symbol: source ID type. See Details for possible values.

reviewed

Translate only reviewed (TRUE), only unreviewed (FALSE) or both (NULL) UniProt records.

organism

Integer, NCBI Taxonomy ID of the organism (by default 9606 for human).

Value

A data frame (tibble) with columns `From` and `To`, UniProt IDs and the corresponding foreign IDs, respectively.

Details

For both source and target ID type, this function accepts column codes used by UniProt and some simple shortcuts defined here. For the UniProt codes please refer to https://www.uniprot.org/help/uniprotkb The shortcuts are entrez, genesymbol, genesymbol_syn (synonym gene symbols), hgnc, embl, refseqp (RefSeq protein), enst (Ensembl transcript), uniprot_entry (UniProtKB AC, e.g. EGFR_HUMAN), protein_name (full name of the protein), uniprot (UniProtKB ID, e.g. P00533). For a complete table please refer to translate_ids.

See also

Examples

uniprot_entrez <- uniprot_full_id_mapping_table(to = 'entrez')
uniprot_entrez
#> # A tibble: 19,078 × 2
#>    From       To       
#>    <chr>      <chr>    
#>  1 A0A087X1C5 1564     
#>  2 A0A0B4J2F0 101928527
#>  3 A0A0B4J2F2 102724428
#>  4 A0A0K2S4Q6 100130520
#>  5 A0A0U1RRE5 550643   
#>  6 A0AV02     84561    
#>  7 A0AV96     54502    
#>  8 A0AVF1     79989    
#>  9 A0AVI4     92305    
#> 10 A0AVK6     79733    
#> # ℹ 19,068 more rows
# # A tibble: 20,723 x 2
#    From   To
#    <chr>  <chr>
#  1 Q96R72 NA
#  2 Q9UKL2 23538
#  3 Q9H205 144125
#  4 Q8NGN2 219873
#  5 Q8NGC1 390439
# # . with 20,713 more rows