Skip to contents

Get Functional Enrichment

Source: R/stringdb.R
rba_string_enrichment.Rd

STRING cross-references proteins with several annotation resources. (See 'Details' section). Provide an input protein set and, optionally, a background protein set to perform an enrichment test and retrieve enriched terms with their associated statistics. 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.)

background

Character vector: A set of STRING protein IDs to be used as the statistical background (or universe) when computing term p-values. Only STRING IDs are accepted. See rba_string_map_ids to map your IDs.

split_df

Logical: (default = TRUE) Split results into a list of data frames by category; otherwise, return one data frame.

...

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

Value

A data frame in which each row is an enriched term with a raw p-value below 0.1 and the columns contain the term category, description, gene counts, p-value, FDR, and other pertinent information. If split_df = TRUE, a list of data frames split by category is returned.

Details

STRING currently returns enrichment results from Gene Ontology (GO), KEGG pathways, UniProt Keywords, PubMed publications, Pfam domains, InterPro domains, and SMART domains.
STRING returns only terms with a raw p-value below 0.1. To retrieve annotations without filtering by enrichment p-value, 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, rba_string_functional_terms

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

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)
# }