ggpicrust2_extended {ggpicrust2} | R Documentation |
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)
[Package ggpicrust2 version 2.3.2 Index]