run_simplify_enrichment {GeneSelectR}

Run simplifyGOFromMultipleLists with specified measure and method

Description

This function is simply a wrapper for the simplifyGOFromMultipleLists function in the simplifyEnrichment package, created for the ease of data input. All credit for the underlying functionality goes to the authors of the simplifyEnrichment package.

Usage

run_simplify_enrichment(
  fs_GO_results,
  padj_column = "p.adjust",
  padj_cutoff,
  ont,
  measure,
  method,
  ...
)

Arguments

fs_GO_results

A list of dataframes containing GO enrichment results for feature selection methods. The GO object for the simplifyGOFromMultipleLists function.

padj_column

Character. The column name for the p-value adjustment.

padj_cutoff

Numeric. The cutoff for the p-value adjustment.

ont

Character. The ontology for the simplifyGOFromMultipleLists function.

measure

Character. The semantic similarity measure for the simplifyGOFromMultipleLists function.

method

Character. The clustering method for the simplifyGOFromMultipleLists function.

...

Other parameters that can be passed to simplifyGOFromMultipleLists

Value

The result of the simplifyGOFromMultipleLists function, typically comprising a heatmap or other visualization that displays the simplified GO enrichment results. The specific output format depends on the chosen semantic similarity measure and clustering method.

References

For more information on the simplifyEnrichment package, see the original publication: Gu Z, Hübschmann D. simplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results. Genomics Proteomics Bioinformatics. 2023 Feb;21(1):190-202. doi: 10.1016/j.gpb.2022.04.008. Epub 2022 Jun 6. PMID: 35680096; PMCID: PMC10373083.

Examples

# Mock GO enrichment results for two feature selection methods
fs_GO_results <- list(
  method1 = list(result = data.frame(GO_ID = c("GO:0008150", "GO:0009987"),
                                    Description = c("Biological Process 1", "Biological Process 2"),
                                    'p.adjust' = c(0.01, 0.02))),
  method2 = list(result = data.frame(GO_ID = c("GO:0008150", "GO:0008152"),
                                    Description = c("Biological Process 1", "Biological Process 3"),
                                    'p.adjust' = c(0.03, 0.04)))
)

# Run the wrapper function with mock data
enrichment_result <- run_simplify_enrichment(fs_GO_results,
                                             padj_column = 'p.adjust',
                                             padj_cutoff = 0.05,
                                             ont = "BP",
                                             measure = "Wang",
                                             method = "kmeans")
print(enrichment_result)