Annotate GSEA results with pathway information

This function adds pathway annotations to GSEA results, including pathway names, descriptions, and classifications.

Usage

gsea_pathway_annotation(gsea_results, pathway_type = "KEGG")

Arguments

gsea_results

A data frame containing GSEA results from the pathway_gsea function

pathway_type

A character string specifying the pathway type: "KEGG", "MetaCyc", or "GO"

Value

A data frame with annotated GSEA results

Details

The pathway_id column must contain non-empty values without NA. Unknown but non-empty pathway IDs are retained as their own display names when no reference annotation is found.

Examples

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

# Prepare abundance data
abundance_data <- as.data.frame(ko_abundance)
rownames(abundance_data) <- abundance_data[, "#NAME"]
abundance_data <- abundance_data[, -1]

# Run GSEA analysis (using camera method - recommended)
gsea_results <- pathway_gsea(
  abundance = abundance_data,
  metadata = metadata,
  group = "Environment",
  pathway_type = "KEGG",
  method = "camera"
)

# Annotate results
annotated_results <- gsea_pathway_annotation(
  gsea_results = gsea_results,
  pathway_type = "KEGG"
)
} # }