library(org.Hs.eg.db)
library(KEGG.db)
tmp=toTable(org.Hs.egPATH)
write.table(tmp,'kegg2gene.list.txt',quote = F,row.names = F)
library("hgu95av2.db")
ls('package:hgu95av2.db')
universeGeneIds <- unique(mappedRkeys(hgu95av2ENTREZID))
write.table(universeGeneIds,'universeGeneIds.txt',quote = F,row.names = F,col.names = F)
set.seed('123456.789')#定义一个种子，下面的随机就不会变了
diff_gene = sample(universeGeneIds,300)
write.table(diff_gene,'diff_gene.txt',quote = F,row.names = F,col.names = F)
library(GOstats)
annotationPKG='org.Hs.eg.db'
hyperG.params = new("KEGGHyperGParams", geneIds=diff_gene, universeGeneIds=universeGeneIds, annotation=annotationPKG, categoryName="KEGG", pvalueCutoff=1, testDirection = "over")
KEGG.hyperG.results = hyperGTest(hyperG.params);
htmlReport(KEGG.hyperG.results, file="kegg.enrichment.html", summary.args=list("htmlLinks"=TRUE))
library(clusterProfiler)
kk <- enrichKEGG(gene = diff_gene,
universe=universeGeneIds,
organism = 'hsa',
pvalueCutoff = 1,qvalueCutoff=1)
y_results=summary(kk)
