This function calls STRING's API to map a set of common gene or protein identifiers to STRING identifiers. Although STRING services accept a variety of identifiers, the STRING API documentation recommends mapping them to STRING identifiers before using other STRING functions.
Arguments
- ids
Character or Numeric: Your common gene/protein identifier(s) to be mapped.
- species
Numeric: (optional) NCBI Taxonomy identifier; Human Taxonomy ID is 9606. (Recommended, but optional.)
- echo_query
Logical: (default =
TRUE) Include your input IDs as a column of the results.- limit
Numeric: (optional) Deprecated: Retained temporarily for backward compatibility. STRING v12 returns only the single best match per input ID, so this argument has no effect.
- ...
rbioapi option(s). See
rba_options's arguments manual for more information on available options.
Value
A data frame with at most one mapped STRING ID per input ID and
other pertinent information. The queryIndex column contains the
zero-based position of each resolved ID in the input vector. Unresolved
inputs are omitted; if none can be resolved, a zero-row data frame
retaining the response columns is returned.
Corresponding API Resources
"POST https://string-db.org/api/tsv/get_string_ids?identifiers= {your_identifiers}&{optional_parameters}"
References
Damian Szklarczyk, Katerina Nastou, Mikaela Koutrouli, Rebecca Kirsch, Farrokh Mehryary, Radja Hachilif, Dewei Hu, Matteo E Peluso, Qingyao Huang, Tao Fang, Nadezhda T Doncheva, Sampo Pyysalo, Peer Bork, Lars J Jensen, Christian von Mering, The STRING database in 2025: protein networks with directionality of regulation, Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D730–D737, https://doi.org/10.1093/nar/gkae1113
See also
Other "STRING":
rba_string_annotations(),
rba_string_enrichment(),
rba_string_enrichment_image(),
rba_string_enrichment_ppi(),
rba_string_functional_terms(),
rba_string_homology_inter(),
rba_string_homology_intra(),
rba_string_interaction_partners(),
rba_string_interactions_network(),
rba_string_network_image(),
rba_string_version()
Examples
# \donttest{
rba_string_map_ids(ids = c("TP53", "TNF", "EGFR"), species = 9606)
# }