Retrieves an identifier translation table from the UniProt ID Mapping service (https://www.uniprot.org/help/id_mapping).
Arguments
- identifiers
Character vector of identifiers
- from
Character or symbol: type of the identifiers provided. See Details for possible values.
- to
Character or symbol: identifier type to be retrieved from UniProt. See Details for possible values.
- chunk_size
Integer: query the identifiers in chunks of this size. If you are experiencing download failures, try lower values.
Value
A data frame (tibble) with columns `From` and `To`, the identifiers provided and the corresponding target IDs, respectively.
Details
This function uses the uploadlists service of UniProt to obtain identifier
translation tables. The possible values for `from` and `to` are the
identifier type abbreviations used in the UniProt API, please refer to
the table here: uniprot_idmapping_id_types or
the table of synonyms supported by the current package:
translate_ids.
Note: if the number of identifiers is larger than the chunk size the log
message about the cache origin is not guaranteed to be correct (most
of the times it is still correct).
Examples
uniprot_genesymbol <- uniprot_id_mapping_table(
c('P00533', 'P23771'), uniprot, genesymbol
)
uniprot_genesymbol
#> # A tibble: 2 × 2
#> From To
#> <chr> <chr>
#> 1 P00533 EGFR
#> 2 P23771 GATA3
# # A tibble: 2 x 2
# From To
# <chr> <chr>
# 1 P00533 EGFR
# 2 P23771 GATA3