Skip to contents

Maps Molecule Identifiers

Source: R/reactome_analysis.R
rba_reactome_analysis_mapping.Rd

Use this function to map molecule identifiers of different species to Reactome Identifiers.

Usage

rba_reactome_analysis_mapping(
  input,
  input_format = NULL,
  projection = TRUE,
  interactors = FALSE,
  ...
)

Arguments

input

Character or Numeric vector: A vector, local file path or URL that points to your identifiers list.

input_format

Character: (optional) This function will automatically identify your supplied input's format. To be explicit, set this argument to one of:

  • "vector": If you supplied a simple vector (numeric or character) as input.

  • "file": If you supplied a local file path pointing to a correctly-formatted text file.

  • "url": If you supplied an HTTP or HTTPS URL pointing to a correctly-formatted text file.

An explicit value takes precedence. Otherwise, HTTP and HTTPS addresses are identified first, followed by existing local files, and then other non-empty character or numeric inputs as identifier vectors.

projection

Logical: (default = TRUE) Should non-human identifiers be projected to their human equivalents? (using Reactome orthology data)

interactors

Logical: (default = FALSE) Should IntAct interaction data be included?

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

List containing your identifiers and the IDS and resources they are mapped to.

Corresponding API Resources

"POST https://reactome.org/AnalysisService/mapping/form"
"POST https://reactome.org/AnalysisService/mapping/form/projection"
"POST https://reactome.org/AnalysisService/mapping/url"
"POST https://reactome.org/AnalysisService/mapping/url/projection"

References

  • Ragueneau, E., Gong, C., Sinquin, P., Sevilla, C., Beavers, D., Grentner, A., ... D’Eustachio, P. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Res., 54(D1), D673–D681. doi: 10.1093/nar/gkaf1223

  • Griss, J., Viteri, G., Sidiropoulos, K., Nguyen, V., Fabregat, A., & Hermjakob, H. (2020). ReactomeGSA—Efficient Multi-Omics Comparative Pathway Analysis. Molecular & Cellular Proteomics, 19(12), 2115–2125. doi: 10.1074/mcp.TIR120.002155

  • Reactome Analysis Services API Documentation

  • Citations note on Reactome website

See also

Other "Reactome Analysis Service": rba_reactome_analysis(), rba_reactome_analysis_download(), rba_reactome_analysis_import(), rba_reactome_analysis_pdf(), rba_reactome_analysis_species(), rba_reactome_analysis_token()

Examples

if (FALSE) { # \dontrun{
rba_reactome_analysis_mapping(c("Q8SQ34", "cd40"))
} # }