小鼠clusterProfiler：GO KEGG

##################################################富集分析

library(clusterProfiler)

#人种 org.Hs.eg.db 小鼠 org.Mm.eg.db 

if (!require("BiocManager", quietly = TRUE))

  install.packages("BiocManager")

BiocManager::install("org.Mm.eg.db")

library(org.Mm.eg.db)

##转换ID

trans <- bitr(gene, fromType="SYMBOL",

              toType="ENTREZID", OrgDb="org.Mm.eg.db")

#######################GO

ego <- enrichGO(gene          = trans$ENTREZID,

                OrgDb         = org.Mm.eg.db,

                ont           = "ALL",

                pAdjustMethod = "BH",

                pvalueCutoff  = 0.05,

                qvalueCutoff  = 1,

                readable      = TRUE)

head(ego@result)

result<-ego@result

write.csv(result,file = 'go.result.csv',quote = F,row.names = T,col.names = T)

##########################KEGG

#organism supported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html'

#hsa 人；mmu 小鼠

kk <- enrichKEGG(gene         = trans$ENTREZID,

                 organism     = 'mmu',

                 pvalueCutoff = 0.05,

                 qvalueCutoff = 1)

tmp <- data.frame(kk)

kkx <- setReadable(kk, 'org.Mm.eg.db', 'ENTREZID')

kk<- data.frame(kkx)

write.csv(kk,file = 'kegg.result.csv',quote = F,row.names = T,col.names = T)