rba_string_interaction_partners {rbioapi} | R Documentation |
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,
...
)
Arguments
ids |
Your protein ID(s). It is strongly recommended to supply
STRING IDs. See |
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:
|
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 |
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
.
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
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
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
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)