Get All STRING Interaction Partners

This function retrieves STRING interactions involving any of your input proteins as one party of the interaction, including interactions with proteins outside the input set.
Given the size of the STRING database, this function can return many interactions. Use the filtering arguments to limit the results.

Usage

rba_string_interaction_partners(
  ids,
  species = NULL,
  required_score = NULL,
  network_type = "functional",
  limit = NULL,
  network_flavor = NULL,
  typed_physical_edges = TRUE,
  typed_regulatory_edges = TRUE,
  ...
)

Arguments

ids

Character or Numeric: Your protein ID(s). It is strongly recommended to supply STRING IDs. See rba_string_map_ids for more information.

species

Numeric: (optional) NCBI Taxonomy identifier; Human Taxonomy ID is 9606. (Recommended, but required if your input contains more than 10 unique IDs.)

required_score

Numeric: (optional) (between 0 and 1000): Minimum interaction score required for an interaction to be included in the returned interactions. If omitted, STRING applies a network-dependent threshold. Common confidence thresholds are 150 (low), 400 (medium), 700 (high), and 900 (highest).

network_type

Character: (default = "functional") One of:

• "functional": (default) Edges indicate both physical and functional associations.

• "physical": Edges indicate that two proteins have a physical interaction or are parts of a complex.

• "regulatory": Directed edges indicate regulation from a source protein to a target protein.

limit

Numeric: (optional) Maximum number of interaction partners returned for each input protein, ordered by confidence. This limits partners rather than response rows; directed or typed results can contain more rows.

network_flavor

Character: (optional) Set to "typed" to retrieve functional, physical, and directional regulatory scores in one response. Requires network_type = "functional". Omit for the ordinary schema.

typed_physical_edges

Logical: (default = TRUE) Include physical scores in a typed response. If FALSE, their columns contain missing values.

typed_regulatory_edges

Logical: (default = TRUE) Include regulatory scores in a typed response. If FALSE, their columns contain missing values.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A data frame in which each row is a network interaction and the columns contain interactor information and interaction scores. Regulatory and typed requests use the corresponding schemas described in rba_string_interactions_network. Missing typed evidence scores are numeric NA.

Details

To retrieve only interactions among the input proteins, see rba_string_interactions_network.

Corresponding API Resources

"POST https://string-db.org/api/{output-format}/interaction_partners? 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

• STRING API Documentation

• Citations note on STRING website

See also

rba_string_map_ids, rba_string_interactions_network, rba_string_network_image, rba_string_enrichment_ppi

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_interactions_network(), rba_string_map_ids(), rba_string_network_image(), rba_string_version()

Examples

# \donttest{
rba_string_interaction_partners(ids = c("9606.ENSP00000269305",
    "9606.ENSP00000398698",
    "9606.ENSP00000275493"),
    network_type = "functional")
# }
# \donttest{
    rba_string_interaction_partners(ids = "9606.ENSP00000269305",
    species = 9606,
    required_score = 700)
# }
# \donttest{
## Limit partners per input protein; directed results can contain more rows
rba_string_interaction_partners(
    ids = "TP53",
    species = 9606,
    network_type = "regulatory",
    limit = 5
)
# }