ggpicrust2_extended: Integrated analysis with ggpicrust2 including GSEA

In ggpicrust2: Make 'PICRUSt2' Output Analysis and Visualization Easier

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())

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()

Value

A list containing ggpicrust2 and GSEA results

Examples

## Not run: 
# 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

## End(Not run)

ggpicrust2 documentation built on April 13, 2025, 9:08 a.m.