GO/KEGG富集分析（仅需基因列表）

 #安装

    
 BiocManager::install("org.Gg.eg.db") #鸡全基因组注释R包
    
 BiocManager::install("clusterProfiler")
    
 BiocManager::install("enrichplot")
    
 install.packages("ggplot2")
    
  
    
 #加载所需要的包
    
 library("clusterProfiler")
    
 library("org.Gg.eg.db")
    
 library("enrichplot")
    
 library("ggplot2")
    
  
    
 #文件预处理
    
 ##输入文件
    
 setwd("C:\ Users\ 64151\ Desktop\ GO")
    
 inputFile="down_GO.txt"
    
 rt=read.table(inputFile,sep="\t",check.names = F,header=F)
    
 ##获取基因列表
    
 genes=as.vector(rt[,1])
    
 ##找基因对应的id
    
 entrezIDs <- mget(genes, org.Gg.egSYMBOL2EG,ifnotfound = NA)
    
 entrezIDs <- as.character(entrezIDs)
    
 ##输出基因+id文件
    
 out=cbind(rt,entrezID=entrezIDs)
    
 colnames(out)[1]="Gene"
    
 write.table(out,file="id.txt",sep = "\t",quote= F,row.names = F)
    
    
    
    
    R
    
    
![](https://ad.itadn.com/c/weblog/blog-img/images/2025-08-17/4yM5mvgzihOETLpS8HbZVG1wkQnt.png)

 ##读取id.txt文件

    
 rt=read.table("id.txt",sep="\t",header=T,check.names=F)  
    
 ##去除基因id为NA的基因
    
 rt=rt[is.na(rt[,"entrezID"])==F,]   
    
 gene=rt$entrezID
    
  
    
 #GO分析
    
 kk <- enrichGO(gene = gene, 
    
            OrgDb = org.Gg.eg.db, # 参考基因组 
    
            pvalueCutoff =0.5, # P值阈值
    
            qvalueCutoff =1, # qvalue是P值的校正值
    
            ont="all", # 分三个层面来阐述基因功能，生物学过程（BP），细胞组分（CC），分子功能（MF）
    
            readable =T) # 是否将基因id转换为基因名
    
 write.table(kk,file="GO_result.txt",sep="\t",quote=F,row.names = F)  #保存富集结果
    
  
    
 #做图
    
 ##柱状图
    
 pdf(file="GO_barplot.pdf",width = 10,height = 13)
    
 barplot(kk, drop = TRUE, showCategory =10,label_format=50,split="ONTOLOGY") + facet_grid(ONTOLOGY~., scale='free')
    
 dev.off()
    
 ##气泡图
    
 pdf(file="GO_bubble.pdf",width = 10,height = 13)
    
 dotplot(kk,showCategory = 10,label_format=50,split="ONTOLOGY",orderBy = "GeneRatio") + facet_grid(ONTOLOGY~., scale='free')
    
 dev.off()
    
  
    
 #KEGG分析
    
 kk <- enrichKEGG(gene = gene,
    
              organism = "gga",
    
              pvalueCutoff =0.05, 
    
              qvalueCutoff =1)   
    
 write.table(kk,file="KEGG_result.txt",sep="\t",quote=F,row.names = F)                          #保存富集结果
    
  
    
 #做图
    
 ##柱状图
    
 pdf(file="KEGG_barplot.pdf",width = 10,height = 13)
    
 barplot(kk, drop = TRUE, showCategory = 30)
    
 dev.off()
    
 ##气泡图
    
 pdf(file="KEGG_bubble.pdf",width = 10,height = 5)
    
 dotplot(kk, showCategory = 30,label_format=50,orderBy = "GeneRatio")
    
 dev.off()
    
    
    
    
    R
    
    
![](https://ad.itadn.com/c/weblog/blog-img/images/2025-08-17/dmR6jzO8JxtgFGwoT7UiPkCLBrEn.png)