uniprot_id_mapping_table: ID translation data from UniProt ID Mapping

In saezlab/OmnipathR: OmniPath web service client and more

ID translation data from UniProt ID Mapping

Description

Retrieves an identifier translation table from the UniProt ID Mapping service (https://www.uniprot.org/help/id_mapping).

Usage

uniprot_id_mapping_table(identifiers, from, to, chunk_size = NULL)

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.

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).

Value

A data frame (tibble) with columns 'From' and 'To', the identifiers provided and the corresponding target IDs, respectively.

See Also

translate_ids

Examples

uniprot_genesymbol <- uniprot_id_mapping_table(
    c('P00533', 'P23771'), uniprot, genesymbol
)
uniprot_genesymbol
# # A tibble: 2 x 2
#   From   To
#   <chr>  <chr>
# 1 P00533 EGFR
# 2 P23771 GATA3

saezlab/OmnipathR documentation built on Nov. 10, 2024, 11:02 p.m.