GO分析-KEGG

代码如下，谢谢指导

DEG_symbolid2$g <- ifelse(DEG_symbolid2$pvalue > 0.05, "stable",
                          ifelse(DEG_symbolid2$log2FoldChange > logFC_t,"up",
                                 ifelse(DEG_symbolid2$log2FoldChange <logFC_t,"down","stable")))
DEG1 <- DEG_symbolid2
gene_up <- DEG1[DEG1$g == "up", "entrezgene_id"] 
gene_down <- DEG1[DEG1$g == "down","entrezgene_id" ]
gene_diff <- c(gene_up,gene_down)
gene_all <- as.character(DEG1[,"entrezgene_id"])
geneList <- DEG1$log2FoldChange
names(geneList)=DEG1$entrezgene_id
geneList=sort(geneList,decreasing = T)

 if(F){
    go_enrich_results <- lapply( g_list , function(gene) {
      lapply( c('BP','MF','CC') , function(ont) {
        cat(paste('Now process ',ont ))
        ego <- enrichGO(gene          = gene,
                        universe      = gene_all,
                        OrgDb         = org.Hs.eg.db,
                        ont           = ont ,
                        pAdjustMethod = "BH",
                        pvalueCutoff  = 0.99,
                        qvalueCutoff  = 0.99,
                        readable      = TRUE)
        
        print( head(ego) )
        return(ego)
      })
    })
    save(go_enrich_results,file = 'go_enrich_results.Rdata')  
  }
  
  
  load(file = 'go_enrich_results.Rdata')
  n1= c('gene_up','gene_down','gene_diff')
  n2= c('BP','MF','CC') 
  for (i in 1:3){
    for (j in 1:3){
      fn=paste0('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()
    }
  }

input：

dotplot_gene_diff_BP.png
dotplot_gene_diff_CC.png
dotplot_gene_diff_MF.png

生物学意义：BP,CC,MF
这些挑选出来的差异化基因主要是富集在哪些通路上。

---

KEGG通路

kk_gse <- gseKEGG(geneList     = geneList,
                  organism     = 'hsa',
                  nPerm        = 1000,
                  minGSSize    = 120,
                  pvalueCutoff = 0.9,
                  verbose      = FALSE)

head(kk_gse)[,1:6]
emapplot(kk_gse,  showCategory = 100)
cnetplot(kk_gse, showCategory = 5)

input：

image.png image.png

谢谢指导

代码参考生信技能树，感谢