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Retrieving Functional Annotation

Source: R/stringdb.R
rba_string_annotations.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 retrieve full set of terms (annotations) pertinent to your input proteins in each database, among with information for each term.

Usage

rba_string_annotations(
  ids,
  species = NULL,
  allow_pubmed = FALSE,
  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.

species

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

allow_pubmed

logical: (default = FALSE) PubMed usually assigns a large number of reference publications to each protein. In order to reduce the output size, PubMed's results will be excluded from the results, unless stated otherwise by setting this argument to TRUE.

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 data frame which every row is an assigned terms and the columns are the terms category, description, number of genes, 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 return a full list of the terms containing your supplied proteins. To perform enrichment and only retrieve a enriched subset of the terms, use rba_string_enrichment.

Corresponding API Resources

"POST https://string-db.org/api/{output_format}/functional_annotation? 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_enrichment

Other "STRING": rba_string_enrichment(), 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()

Examples

# \donttest{
rba_string_annotations(ids = "TP53", species = 9606)
# }