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Run Simple Metabolite Set Enrichment Analysis (MSEA)

Run_simple_MSEA.Rd

This function performs simple metabolite set enrichment analysis on a given dataset. It ensures that the ranking conditions are set properly and conducts the enrichment analysis using either the KS-signed method or fgsea.

Usage

Run_simple_MSEA(object, min_pathway_size = 3)

Arguments

object

A S2IsoMEr object initialized by initEnrichment containing the necessary data and parameters, including annotations, annotation weights, rankings, pathway list, and additional settings.

min_pathway_size

An integer specifying the minimum number of metabolites that must be present in a given term for it to be considered.

Value

A list containing the results of the enrichment analysis, including:

  • enrichment results

  • the comparison conditions

Details

This function performs a bootstrapped metabolite set enrichment analysis by resampling the annotations and calculating enrichment scores for each bootstrap sample. It handles both KS-signed method](https://github.com/franapoli/signed-ks-test/blob/master/signed-ks-test.R) or fgsea methods for enrichment analysis and returns a comprehensive summary of the results.

References

Korotkevich G, Sukhov V, Sergushichev A (2019). “Fast gene set enrichment analysis.” bioRxiv. doi:10.1101/060012, http://biorxiv.org/content/early/2016/06/20/060012.

Napoli F (2017). “signed-ks-test.” https://github.com/franapoli/signed-ks-test/blob/master/signed-ks-test.R.

Examples

if (FALSE) { # \dontrun{
data("example_MSEA_obj")
result <- Run_simple_MSEA(object = example_MSEA_obj, n_bootstraps = 50)
} # }