Skip to contents

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 = "id",
  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: 19,195 × 2
#>    From   To   
#>    <chr>  <chr>
#>  1 Q96JT2 85414
#>  2 Q9UP95 6560 
#>  3 Q08357 6575 
#>  4 O94855 9871 
#>  5 Q8N2U9 80148
#>  6 Q96CW6 84138
#>  7 Q01959 6531 
#>  8 Q9NQ03 85508
#>  9 P48061 6387 
#> 10 Q15047 9869 
#> # … with 19,185 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