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Import Saved Analysis JSON to Reactome

Source: R/reactome_analysis.R
rba_reactome_analysis_import.Rd

If you have a JSON file of analysis results (only obtained via rba_reactome_analysis_download with the result argument set to "results", or "results_gz"), you can import the results back to Reactome and retrieve a token.
This is useful when you want to use other Reactome services which require a token but you do not have a token or your token has been expired (i.e. more than 7 days passed from your analysis).

Usage

rba_reactome_analysis_import(input, input_format = NULL, ...)

Arguments

input

A local file path or URL that points to your -optionally gzipped- JSON file.

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:

  • "file": If you supplied a local file path pointing to the JSON file.

  • "url": If you supplied a URL pointing to the JSON file.

...

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

Value

A list containing the new token and other information of your imported results.

Corresponding API Resources

"GET https://reactome.org/AnalysisService/import/"
"GET https://reactome.org/AnalysisService/import/form"
"GET https://reactome.org/AnalysisService/import/url"

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_mapping(), rba_reactome_analysis_pdf(), rba_reactome_analysis_species(), rba_reactome_analysis_token()

Examples

if (FALSE) { # \dontrun{
rba_reactome_analysis_import("c:/rbioapi/res.json")
} # }
if (FALSE) { # \dontrun{
rba_reactome_analysis_import("https://qaz.com/res.json.gz")
} # }