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Getting Functional Enrichment

Source: R/stringdb.R
rba_string_enrichment.Rd

STRING cross-reference the proteins with several databases (see "Details" section). By providing your input set o proteins (and optionally background or universe protein set), you can use this function to perform enrichment test and retrieve a list of enriched terms in each database, among with pertinent information for each term. Use rba_string_enrichment_image to retrieve the analysis results as a plot.

Usage

rba_string_enrichment(
  ids,
  species = NULL,
  background = NULL,
  split_df = TRUE,
  ...
)

Arguments

ids

Your protein ID(s). It is strongly recommended to supply STRING IDs. See rba_string_map_ids for more information. Note that if only one id is supplied, STRING expands the network by 10 proteins.

species

Numeric: NCBI Taxonomy identifier; Human Taxonomy ID is 9606. (Recommended, but optional if your input is less than 100 IDs.)

background

character vector: A set of STRING protein IDs to be used as the statistical background (or universe) when computing P-value for the terms. Only STRING IDs are acceptable. (See rba_string_map_ids to map your IDs.)

split_df

(logical, default = TRUE), If TRUE, instead of one data frame, results from different categories will be split into multiple data frames based on their 'category'.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A list of data frames which every row is an enriched terms with p-value smaller than 0.1 and the columns are the terms category, description, number of genes, p-value, fdr and other pertinent information.

Details

STRING currently maps to and retrieve enrichment results based on Gene Ontology (GO), KEGG pathways, UniProt Keywords, PubMed publications, Pfam domains, InterPro domains, and SMART domains.
Note that this function will only return the enriched terms pertinent to your proteins that have a p-value lesser than 0.1. To retrieve a full list of the terms -unfiltered by enrichment p-values-, use rba_string_annotations.

Corresponding API Resources

"POST https://string-db.org/api/{output_format}/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_annotations, rba_string_enrichment_image

Other "STRING": rba_string_annotations(), rba_string_enrichment_image(), rba_string_enrichment_ppi(), 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()

Other "Enrichment/Over-representation": rba_enrichr(), rba_mieaa_enrich(), rba_panther_enrich(), rba_reactome_analysis(), rba_string_enrichment_image()

Examples

# \donttest{
rba_string_enrichment(ids = c("TP53", "TNF", "EGFR"), species = 9606)
# }