rbioapi: rba_string_map_ids – R documentation

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rba_string_map_ids

Map a Set of Identifiers to STRING Identifiers

Description

This function Calls STRING's API to Convert a set of identifiers to STRING Identifiers. Although You can call STRING services with a variety of common identifiers, It is recommended by STRING's documentations that you first map Your Protein/genes IDs to STRING IDs and then proceed with other STRING's functions.

Usage

rba_string_map_ids(ids, species = NA, echo_query = FALSE, limit = NA, ...)

Arguments

`ids`	Your Common gene/protein Identifier(s) to be mapped.
`species`	Numeric: NCBI Taxonomy identifier; Human Taxonomy ID is 9606. (Recommended, but optional if your input is less than 100 IDs.)
`echo_query`	(default = FALSE) Include your input IDs as a column of the results.
`limit`	(Numeric, Optional) A limit on the number of matches per input ID.
`...`	rbioapi option(s). Refer to `rba_options`'s arguments documentation for more information on available options.

Value

A data frame with the mapped STRING IDs and other pertinent information.

Corresponding API Resources

"POST https://string-db.org/api/[output-format]/get_string_ids?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_map_ids(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