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Get All STRING Interaction Partners

Source: R/stringdb.R
rba_string_interaction_partners.Rd

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,
  ...
)

Arguments

ids

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

species

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

required_score

Numeric (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: 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.

limit

Numeric: Maximum number of interaction partners returned for each input protein, ordered by confidence.

...

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.

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, Rebecca Kirsch, Mikaela Koutrouli, Katerina Nastou, Farrokh Mehryary, Radja Hachilif, Annika L Gable, Tao Fang, Nadezhda T Doncheva, Sampo Pyysalo, Peer Bork, Lars J Jensen, Christian von Mering, The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D638–D646, https://doi.org/10.1093/nar/gkac1000

  • 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)
# }