📖 Introduction | Biomedical Knowledge Mining using GOSemSim and clusterProfiler (yulab-smu.top)

部分使用

#GO classification

library(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)

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