R包clusterProfiler功能富集分析及可视化总结

source("http://www.bioconductor.org/biocLite.R")#启动bioconductor

biocLite("clusterProfiler")#安装clusterProfiler包

library(clusterProfiler)

##文件为一列gene entrezID, 文件名设为 enterz.txt

 

setwd("d:/") #设置目录

getwd() #查看目录

 

biocLite("org.Hs.eg.db")

library(org.Hs.eg.db)

 

ego <- enrichGO(OrgDb="org.Hs.eg.db", gene =genelist, ont = "CC", pvalueCutoff = 0.01, readable= TRUE)#GO富集分析

 

write.csv(summary(ego),"GO-enrich.csv",row.names=F) #写入文件

 

ekk <- enrichKEGG(gene=genelist,organism  = 'hsa', qvalueCutoff = 0.05)#KEGG富集分析

 

write.csv(summary(ekk),"KEGG-enrich.csv",row.names=F) #写入文件

 

dotplot(ego,showCategory=10,title="Enrichment GOTop10") #泡泡图

barplot(ego, showCategory=20,title="EnrichmentGO") #柱状图