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
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.
Value
A data frame which each row is a network interaction and the columns contains interactor information and interaction scores.
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
.
Corresponding API Resources
"POST https://string-db.org/api/[output-format]/ interaction_partners?identifiers=[your_identifiers]&[optional_parameters]"
References
Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T Doncheva, Marc Legeay, Tao Fang, Peer Bork, Lars J Jensen, Christian von Mering, The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D605–D612, https://doi.org/10.1093/nar/gkaa1074
See also
rba_string_map_ids, rba_string_interactions_network
Other "STRING":
rba_string_annotations()
,
rba_string_enrichment_ppi()
,
rba_string_enrichment()
,
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)
# }