bio-pathway-kegg-pathways

## Version Compatibility Reference examples tested with: R stats (base), clusterProfiler 4.10+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # KEGG Pathway Enrichment ## Core Pattern **Goal:** Identify KEGG metabolic and signaling pathways over-represented in a gene list. **Approach:** Test for enrichment using the hypergeometric test via clusterProfiler enrichKEGG against the KEGG online database. **"Find enriched KEGG pathways in my gene list"** → Test whether KEGG pathway gene sets are over-represented among significant genes. ```r library(clusterProfiler) kk <- enrichKEGG( gene = gene_list, # Character vector of gene IDs organism = 'hsa', # KEGG organism code pvalueCutoff = 0.05, pAdjustMethod = 'BH' ) ``` ## Prepare Gene List **Goal:** Extract significant Entrez gene IDs from DE results in the format required by enrichKEGG. **Approach:** Filter by significance thresholds and convert gene symbols to Entrez IDs (KEGG requires NCBI Entrez). ```r library(org.Hs.eg.db) de_results <- read.csv('de_results.csv') sig_genes <- de_results$gene_id[de_results$padj < 0.05 & abs(de_results$log2FoldChange) > 1] # KEGG requires NCBI Entrez gene IDs (kegg, ncbi-geneid) gene_...