ggpicrust2 (version 2.1.2)

ggpicrust2_extended: Integrated analysis with ggpicrust2 including GSEA

Description

This function extends the ggpicrust2 functionality to include Gene Set Enrichment Analysis (GSEA).

Usage

ggpicrust2_extended(..., run_gsea = FALSE, gsea_params = list())

Value

A list containing ggpicrust2 and GSEA results

Arguments

...

Parameters passed to ggpicrust2()

run_gsea

Logical value indicating whether to perform GSEA analysis

gsea_params

List of parameters to pass to pathway_gsea()

Examples

if (FALSE) {
# Load example data
data(ko_abundance)
data(metadata)

# Run integrated analysis
integrated_results <- ggpicrust2_extended(
  data = ko_abundance,
  metadata = metadata,
  group = "Environment",
  pathway = "KO",
  daa_method = "LinDA",
  ko_to_kegg = TRUE,
  run_gsea = TRUE,
  gsea_params = list(
    method = "fgsea",
    rank_method = "signal2noise",
    nperm = 1000
  )
)

# Access DAA results
daa_results <- integrated_results$daa_results

# Access GSEA results
gsea_results <- integrated_results$gsea_results

# Access plots
daa_plot <- integrated_results$daa_plot
gsea_plot <- integrated_results$gsea_plot
}