Generate a GSEA Report — run_gsea • SplineOmics

This function generates a Gene Set Enrichment Analysis (GSEA) report based on clustered hit levels, gene data, and specified databases. It processes the input data, manages GSEA levels, and produces an HTML report with plots.

Usage

run_gsea(
  levels_clustered_hits,
  databases,
  report_info,
  clusterProfiler_params = NA,
  plot_titles = NA,
  universe = NULL,
  report_dir = here::here()
)

Arguments

levels_clustered_hits: A list of clustered hits at different levels.
databases: A list of databases for the gene set enrichment analysis.
report_info: A list containing information for the report generation.
clusterProfiler_params: Additional parameters for the GSEA analysis, default is NA. Those include adj_p_value, pAdjustMethod, etc (see clusterProfiler documentation).
plot_titles: Titles for the plots, default is NA.
universe: Enrichment background data, default is NULL.
report_dir: Directory where the report will be saved, default is `here::here()`.

Value

A list of plots generated for the GSEA report.