clusterprofiler包进行GO与KEGG富集分析

RNA-seq寻找到差异基因后，对比GO与KEGG库进行差异分析

rm(list = ls())
options(stringsAsFactors = F)
DEG <- read.csv('./DEGs_filter.csv', header  = T, row.names = 1)
gene <- DEG$Entrezid

genelist <- data.frame(DEG$Entrezid, DEG$log2FoldChange)
head(genelist)
dim(genelist)
genelist <- genelist[order(genelist$DEG.log2FoldChange, decreasing = T),]
head(genelist)
dim(genelist)
gene_fc <- genelist$DEG.log2FoldChange
names(gene_fc) <- genelist$DEG.Entrezid


library(clusterProfiler)
library(org.Mm.eg.db)
library(org.Hs.eg.db)


#### GO: Over-Representation Analysis  ####

# Biological Process
ego_BP <- enrichGO(gene = gene,
                keyType ='ENTREZID' , 
                ont="BP",
                OrgDb = org.Mm.eg.db,
                pAdjustMethod = 'BH',
                pvalueCutoff = 0.01,
                qvalueCutoff =0.05,
                readable = T)
ego_BP2 <- simplify(ego_BP, cutoff=0.7, by='p.adjust', select_fun = min)

write.csv(ego_BP2@result, './GO ORA_BP.csv')

png('GO_BP_barplot.png')
barplot(ego_BP2, showCategory = 10, title = 'Biological Process of TOP10')
dev.off()

png('GO_BP_dotplot.png')
dotplot(ego_BP2, showCategory = 10, title = 'Biological Process of TOP10')
dev.off()

# Cellular Component
ego_CC <- enrichGO(gene = gene,
                   keyType ='ENTREZID' , 
                   ont="CC",
                   OrgDb = org.Mm.eg.db,