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Map a Set of Identifiers to STRING Identifiers

Source: R/stringdb.R
rba_string_map_ids.Rd

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. The output are sorted to have the best matches first.

...

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, 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

Other "STRING": rba_string_annotations(), 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_network_image(), rba_string_version()

Examples

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