自己制作gmt，做GSEA，内含“clusterProfiler

rm(list = ls())
options(stringsAsFactors = F)

#读取excel
#install.packages("readxl")
library(readxl)
mRNA = read_excel("VDR target genes.xlsx",sheet = 1) 
##制作gmt文档
gset <- c("VDR_target_geneset","NA",mRNA$gene)
gset <- gset%>% 
  as.data.frame() %>% 
  t()
write.table(gset,file = "VDR_Target_geneset.gmt",sep = "\t",row.names = F,col.names = F,quote = F)

kegmt<-read.gmt("VDR_Target_geneset.gmt")

 ##制作差异表达谱genelist

library(msigdbr)
library(fgsea)
library(org.Hs.eg.db)
library(dplyr)
library(clusterProfiler)


###此处加载你的差异表达谱

## 1.按照logFC进行排序
geneList1 <- DEG$logFC
## 2.命名
names(geneList1) = DEG$Gene.Symbol
## 3.排序很重要
geneList1 = sort(geneList1, decreasing = TRUE)
head(geneList1)

##4读取gmt基因集下载于https://www.gsea-msigdb.org/gsea/downloads.jsp
#kegmt<-read.gmt("HALLMARK_WNT_BETA_CATENIN_SIGNALING.v2023.1.Hs.gmt") #读gmt文件


##GSEA
KEGG<-GSEA(geneList1,TERM2GENE = kegmt,minGSSize = 1,
           maxGSSize = 500,
           pvalueCutoff =1) #GSEA分析

##画图 base size是字体大小
library(enrichplot)
gseaplot2(KEGG,1,color="red", base_size = 30,pvalue_table = T)

clusterProfiler包老版本已经不能使用，会报错

a5cd8f343c585038d59f37cfe511b9e.png
80bf904d1425aeb41aedd28fdff76ca.png

此时运行以下代码进行安装，更新“clusterProfiler”，里面有很多依赖包也同时需要更新。

devtools::install_github('YuLab-SMU/clusterProfiler')