rbioapi: rba_string_interactions_network – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

rba_string_interactions_network

Get STRING Network Interactions

Description

This function will retrieve Sting interaction pairs among your input protein ids, with the combined score and separate score for each STRING score channels. You can further expand your network to a defined size by providing "add_node" parameter.

Usage

rba_string_interactions_network(
  ids,
  species = NA,
  required_score = NA,
  add_nodes = NA,
  network_type = "functional",
  ...
)

Arguments

`ids`	Your protein IDs. 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)
`add_nodes`	Numeric: Number of neighboring proteins to be added to the network. If none provided by the user, this argument value will depend on the number of provided "ids" argument: Single id: add_node will be set to 10 to retrieve the interaction neighborhood of you input protein. Multiple ids: add_node will be set to 0, thus the output will be the interactions between your input proteins.
`network_type`	should be one of: "functional": (default) The edge's indicate both physical and functional associations. "physical": The edges indicate that two proteins have a physical interaction or are parts of a complex.
`...`	rbioapi option(s). Refer to `rba_options`'s arguments documentation for more information on available options.

Details

Note that this function will return interactions between your set of provided proteins, or at most, expand the interaction network by the given parameters. TO retrieve a list of all possible interacting proteins with your given input, refer to rba_string_interaction_partners.

Value

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

stringId_A: STRING identifier (protein A)
stringId_B:STRING identifier (protein B)
preferredName_A: common protein name (protein A)
preferredName_B: common protein name (protein B)
ncbiTaxonId: NCBI taxon identifier
score: combined score
nscore: gene neighborhood score
fscore: gene fusion score
pscore: phylogenetic profile score
ascore: co-expression score
escore: experimental score
dscore: database score
tscore: textmining score

Corresponding API Resources

"POST https://string-db.org/api/[output-format]/network?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_interactions_network(ids = c("9606.ENSP00000269305",
    "9606.ENSP00000398698",
    "9606.ENSP00000275493"),
    network_type = "functional")


rba_string_interactions_network(ids = c("9606.ENSP00000269305",
    "9606.ENSP00000398698",
    "9606.ENSP00000275493"),
    species = 9606,
    add_nodes = 10)

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release