rbioapi (version 0.8.1)

rba_string_interaction_partners: Get All STRING Interaction Partners

Description

This function will retrieve all the STRING interactions which include your proteins as one party of the interaction. (e.g. interaction between your proteins and every other STRING proteins.)
Given the size of STRING database, this function could return a very long results. See "Arguments" section for information on how to filter the interactions.

Usage

rba_string_interaction_partners(
  ids,
  species = NULL,
  required_score = NULL,
  network_type = "functional",
  limit = NULL,
  ...
)

Value

A data frame which each row is a network interaction and the columns contains interactor information and interaction scores.

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 optional if your input is less than 100 IDs.)

required_score

Numeric: A minimum of interaction score for an interaction to be included in the image. if not supplied, the threshold will be applied by STRING Based in the network. (low Confidence = 150, Medium Confidence = 400, High Confidence = 700, Highest confidence = 900)

network_type

should be one of:

• "functional": (default) The edge's indicate both physical and functional associations.

limit

Limit the number returned interaction partners per each of your input proteins. (e.g. Number of the most confident interaction partner to return per each input protein.)

...

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

Corresponding API Resources

"POST https://string-db.org/api/{output-format}/ interaction_partners?identifiers={your_identifiers}&{optional_parameters}"

Details

Note that this function will retrieve the interactions between your input proteins and every other STRING proteins. To retrieve the interaction among your input protein-set, see rba_string_interactions_network.

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

Other "STRING": rba_string_annotations(), rba_string_enrichment(), rba_string_enrichment_ppi(), 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)
# }