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Get Protein-Protein Interaction Enrichment

Source: R/stringdb.R
rba_string_enrichment_ppi.Rd

STRING compares the interaction pattern of your input proteins with the proteome-wide background interaction distribution to determine whether the protein set contains more interactions than expected.

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 required if your input contains more than 10 unique IDs.)

required_score

Numeric (between 0 and 1000): Minimum interaction score used when calculating PPI enrichment. If omitted, STRING applies a network-dependent threshold. Common confidence thresholds are 150 (low), 400 (medium), 700 (high), and 900 (highest).

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.

Value

A list with protein-protein interaction enrichment results.

Corresponding API Resources

"POST https://string-db.org/api/{output-format}/ppi_enrichment?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

  • STRING API Documentation

  • Citations note on STRING website

See also

rba_string_map_ids, rba_string_interactions_network, rba_string_interaction_partners, rba_string_network_image

Other "STRING": rba_string_annotations(), rba_string_enrichment(), rba_string_enrichment_image(), rba_string_functional_terms(), rba_string_homology_inter(), rba_string_homology_intra(), rba_string_interaction_partners(), rba_string_interactions_network(), rba_string_map_ids(), rba_string_network_image(), rba_string_version()

Examples

# \donttest{
rba_string_enrichment_ppi(ids = c("p53", "BRCA1", "cdk2", "Q99835",
       "CDC42", "CDK1", "KIF23", "PLK1", "RAC2", "RACGAP1"),
    species = 9606)
# }