RIP-Seq(MeRIP-Seq)（7）-- peaks注释
2022-06-19 本文已影响0人
Z_bioinfo
提取peakAnnolist中的基因，结合clusterProfiler包对peaks内的邻近基因进行GO和KEGG富集注释。
library(clusterProfiler)
library("org.Hs.eg.db")
# Run GO enrichment analysis
ego <- enrichGO(unique(peakAnnoList@anno$SYMBOL), keyType = 'SYMBOL', OrgDb = org.Hs.eg.db, ont = "BP", pAdjustMethod = "BH", qvalueCutoff = 0.05)
# Dotplot visualization
dotplot(ego, showCategory=50)
# Multiple samples KEGG analysis
先装R.utils，不然后面会报错，不知道为啥，之前没有出现这个情况，R版本升级之后就出现了这个问题
install.packages("R.utils")
R.utils::setOption("clusterProfiler.download.method",'auto')
kk <- enrichKEGG(unique(peakAnnoList@anno$geneId),organism = 'hsa', pvalueCutoff = 0.05)
dotplot(kk, showCategory = 20, title = "KEGG Pathway Enrichment Analysis")
