gsea_pathway_annotation: Annotate GSEA results with pathway information

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

Annotate GSEA results with pathway information

Description

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

Examples

## Not run: 
# 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
gsea_results <- pathway_gsea(
  abundance = abundance_data,
  metadata = metadata,
  group = "Environment",
  pathway_type = "KEGG",
  method = "fgsea"
)

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

## End(Not run)

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