rbioapi: rba_string_annotations – R documentation

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rba_string_annotations

Retrieving Functional Annotation

Description

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 = NA, allow_pubmed = FALSE, ...)

Arguments

`ids`	Your protein ID(s). It is strongly recommended to provide 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).
`...`	rbioapi option(s). Refer to `rba_options`'s arguments documentation for more information on available options.

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 provided proteins. To perform enrichment and only retrieve a enriched subset of the terms, use rba_string_enrichment.

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.

Corresponding API Resources

"POST https://string-db.org/api/[output_format]/functional_annotation? identifiers=[your_identifiers]&[optional_parameters]"

References

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613. doi: 10.1093/nar/gky1131. PMID: 30476243; PMCID: PMC6323986.
STRING API Documentation

Examples

rba_string_annotations(ids = "TP53", species = 9606)

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release