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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

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

input_format

(Optional) This function will automatically identify your supplied input's format. But in case of unexpected issues or if you want 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 a URL pointing to a correctly-formatted text file.

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

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

References

  • Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

  • Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

  • 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"))
} # }