📖 Introduction | Biomedical Knowledge Mining using GOSemSim and clusterProfiler (yulab-smu.top)
部分使用
#GO classificationlibrary(clusterProfiler)
data(geneList, package="DOSE")
gene <- names(geneList)[abs(geneList) > 2]# Entrez gene ID
head(gene)
ggo <- groupGO(gene = gene,OrgDb = org.Hs.eg.db,ont = "CC",level = 3,readable = TRUE)head(ggo)##############################################################
##KEGG##
library(clusterProfiler)
search_kegg_organism('ece', by='kegg_code')
ecoli <- search_kegg_organism('Escherichia coli', by='scientific_name')
dim(ecoli)data(geneList, package="DOSE")
gene <- names(geneList)[abs(geneList) > 2]kk <- enrichKEGG(gene = gene,organism = 'hsa',pvalueCutoff = 0.05)
head(kk)【精选】RNA 11. SCI 文章中基因表达富集之 GSEA_gsea数据库-CSDN博客
