rbioapi: rba_string_interaction_partners – R documentation

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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. Refer to "Arguments" section for information on how to filter the interactions.

Usage

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

Arguments

`ids`	Your protein ID(s). It is strongly recommended to provide 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 provided, 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). Refer to `rba_options`'s arguments documentation for more information on available options.

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, refer to rba_string_interactions_network.

Value

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

Corresponding API Resources

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

References

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613. doi: 10.1093/nar/gky1131. PMID: 30476243; PMCID: PMC6323986.
STRING API Documentation

Examples

rba_string_interaction_partners(ids = c("9606.ENSP00000269305",
    "9606.ENSP00000398698",
    "9606.ENSP00000275493"),
    network_type = "functional")


    rba_string_interaction_partners(ids = "9606.ENSP00000269305",
    species = 9606,
    required_score = 700)

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release