GO 注釋

ego <- enrichGO(gene          = gene_diff,
                universe      = gene_all,
                OrgDb         = org.Hs.eg.db,
                ont           = 'BP' ,  # 'BP','MF','CC'
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.99,
                qvalueCutoff  = 0.99,
                readable      = TRUE)
enrich_GO=dotplot(ego)
print(enrich_GO)

KEGG注釋

  kk.up <- enrichKEGG(gene         = gene_up,
                      organism     = 'hsa',
                      universe     = gene_all,
                      pvalueCutoff = 0.01,
                      qvalueCutoff =0.01)
  head(kk.up)[,1:6]
  # browseKEGG(kk.up,'hsa05323') ### 查看通路富集圖
  browseKEGG(kk.up,'hsa04512')
  g_kegg_up=dotplot(kk.up)
  print(g_kegg_up)
  kegg_up_dt <- as.data.frame(kk.up)
write.csv(kegg_up_dt,file='kegg_up_dt.csv')

Go注釋批量導(dǎo)出結(jié)果

for (i in 1:3){
  for (j in 1:3){
    fn=paste0('./figure/dotplot_',n1[i],'_',n2[j],'.png')
    cat(paste0(fn,'\n'))
    png(fn,res=150,width = 1080)
    print(dotplot(go_enrich_results[[i]][[j]] ))
    dev.off()
  }
}



for (i in 1:3){
  for (j in 1:3){
    fn=paste0('./figure/dotplot_',n1[i],'_',n2[j],'.csv')
    cat(paste0(fn,'\n'))
    result <- as.data.frame(go_enrich_results[[i]][[j]])[as.data.frame(go_enrich_results[[i]][[j]])$p.adjust< 0.05,]
    write.csv(result,file = fn)
  }
}