Format Enrichment Map Data — enrichmentmap

This function processes and formats GSEA results for visualization in EnrichmentMap.

Usage

enrichmentmap_pip(
  dds,
  org,
  group_by,
  collection = c("HALLMARK", "GOBP", "KEGG", "REACTOME"),
  group_dir,
  save_dir = group_dir,
  save_dir_name = "enrichmentmap"
)

Arguments

dds: DESeq2 object
org: The organism to use, either "human" or "mouse".
collection: Vector of gene set collections to process. Default includes HALLMARK, GOBP, KEGG, and REACTOME
group_dir: Parent directory containing comparison subdirectories. Default is current working directory
save_dir: Directory where the formatted files will be saved. Default is current working directory
save_dir_name: Name of the subdirectory to save files in. Default is "enrichmentmap"

Value

None. Creates formatted files for EnrichmentMap visualization

Examples

if (FALSE) { # \dontrun{
# Format all default collections
enrichmentmap_pip(dds, group_by = "group", group_dir = "results")

# Format specific collections
enrichmentmap_pip(dds, group_by = "group", group_dir = "results", collection = c("HALLMARK", "KEGG"))
} # }