Retrieve human-readable KEGG pathway name to Ensembl gene ID mapping table

getKEGG.R

pkgs <- c("KEGGREST", "org.Mm.eg.db", "tidyverse", "AnnotationDbi")
invisible(lapply(pkgs, function(x) suppressPackageStartupMessages(library(x, character.only = TRUE))))

pathway_id_2_name <- 
  keggList("pathway", "mmu") %>%
  enframe(name = "pathway_id", value = "pathway_name") %>%
  mutate(pathway_id = gsub("mmu", "", pathway_id),
         pathway_name = gsub(" - .*", "", pathway_name))

pathway_2_entrez <- 
  keggLink("pathway", "mmu") %>%
  enframe(name = "entrez_id", value = "pathway_id") %>%
  mutate(pathway_id = gsub("path:mmu", "", pathway_id),
         entrez_id = gsub("mmu:", "", entrez_id))

entrez_to_ensembl <-
  mapIds(org.Mm.eg.db, pathway_2_entrez$entrez_id, "ENSEMBL", "ENTREZID", multiVals = "list") %>%
  enframe(name = "entrez_id", value = "gene_id") %>%
  unnest(cols = gene_id) %>%
  filter(!is.na(gene_id))

kegg_to_ensembl <- 
  entrez_to_ensembl %>%
  left_join(x = ., y = pathway_2_entrez, by = "entrez_id", relationship = "many-to-many") %>% 
  left_join(x = ., y = pathway_id_2_name, by = "pathway_id", relationship = "many-to-many") %>%
  filter(!is.na(gene_id) & !is.na(pathway_name)) %>%
  dplyr::select(pathway_name, gene_id)
  
head(kegg_to_gene)