[KEGGREST] KEGG pathway level 1,2,3를 R에서 다운 받기

KEGGREST 패키지를 사용해서 KEGG pathway의 level1,2,3정보를 다운 받을 수 있다. 

library(KEGGREST)

# 예제 kegg id
ids <- c("ko00564","ko00680","ko00562","ko03030","ko00561")

# kegg database 다운로드
Kegg_results <- list()
for ( i in ids) {
  Kegg_results[[i]] <- tryCatch(keggGet(i), error=function(e) NULL) # https://www.biostars.org/p/366463/
}

# level 1,2,3를 담을 data.frame만들기
keg_ids <- names(Kegg_results)
pathway_tab <-  data.frame(row.names = keg_ids)

# for 문을 이용해서 level데이터 가져오기
for (i in keg_ids){
        pathway_tab[i, "Level1"] <- strsplit( Kegg_results[[i]][[1]]$CLASS, "; ")[[1]][1]
        pathway_tab[i, "Level2"] <- strsplit( Kegg_results[[i]][[1]]$CLASS, "; ")[[1]][2]
        pathway_tab[i, "Level3"] <- Kegg_results[[i]][[1]]$PATHWAY_MAP

}

 

pathway_tab
#                                 Level1                  Level2                         Level3
# ko00564                     Metabolism        Lipid metabolism Glycerophospholipid metabolism
# ko00680                     Metabolism       Energy metabolism             Methane metabolism
# ko00562                     Metabolism Carbohydrate metabolism  Inositol phosphate metabolism
# ko03030 Genetic Information Processing  Replication and repair                DNA replication
# ko00561                     Metabolism        Lipid metabolism        Glycerolipid metabolism

이렇게 kegg의 pathway에 관련된 데이터를 가져와서 정리하였다. 

 

 

 

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| 참고

Chen Yang, Aaron Burberry, Xuan Cao, Jiahao Mai, Fabio Cominelli, Liangliang Zhang. (2023). ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization. arXiv preprint arXiv:2303.10388.