rbioapi: rba_string_enrichment – R documentation

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rba_string_enrichment

Getting Functional Enrichment

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 perform enrichment test and retrieve a list of enriched terms in each database, among with pertinent information for each term.

Usage

rba_string_enrichment(
  ids,
  species = NA,
  background = NA,
  split_df = 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.)
`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. (Refer to `rba_string_map_ids` to map your IDs.)
`split_df`	(logical, default = FALSE), 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). 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 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.

Value

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

Corresponding API Resources

"POST https://string-db.org/api/[output_format]/enrichment?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_enrichment(ids = c("TP53", "TNF", "EGFR"), 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