Map a Set of Identifiers to STRING Identifiers

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 = NULL, echo_query = FALSE, limit = NULL, ...)

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). See rba_options's arguments manual 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

• Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T Doncheva, Marc Legeay, Tao Fang, Peer Bork, Lars J Jensen, Christian von Mering, The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D605–D612, https://doi.org/10.1093/nar/gkaa1074

• STRING API Documentation

• Citations note on STRING website

See also

Other "STRING": rba_string_annotations(), rba_string_enrichment_ppi(), rba_string_enrichment(), rba_string_homology_inter(), rba_string_homology_intra(), rba_string_interaction_partners(), rba_string_interactions_network(), rba_string_network_image(), rba_string_version()

Examples

# \donttest{
rba_string_map_ids(ids = c("TP53", "TNF", "EGFR"), species = 9606)
# }