Even when there is no annotation for your input proteins, STRING can Compare your Given proteins interactions pattern with the background proteome-wide interaction distribution to determine if your given set of proteins are functionally related.
Usage
rba_string_enrichment_ppi(
ids,
species = NULL,
required_score = NULL,
background = 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)
- background
character vector: A set of STRING protein IDs to be used as the background proteome. Only STRING IDs are acceptable. (See
rba_string_map_ids
to map your IDs.)- ...
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]/ppi_enrichment?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
Examples
# \donttest{
rba_string_enrichment_ppi(ids = c("p53", "BRCA1", "cdk2", "Q99835",
"CDC42", "CDK1", "KIF23", "PLK1", "RAC2", "RACGAP1"),
species = 9606)
# }