rbioapi (version 0.8.3)

rba_string_enrichment_ppi: Get Protein-Protein Interaction Enrichment

Description

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,
  ...
)

Value

A list with protein-protein interaction enrichment results.

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, 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

Other "STRING": rba_string_annotations(), rba_string_enrichment(), rba_string_enrichment_image(), 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)
# }