如何批量的对每个cluster findmarker并富集
library(clusterProfiler)
library(ggplot2)
for(j in 0:15) {
cluster.markers <- FindMarkers(object = sce_endo, ident.1 = j, logfc.threshold = 0.25, test.use = "bimod", only.pos = TRUE)
cluster <- row.names.data.frame(cluster.markers)
cluster = bitr(cluster,fromType = "SYMBOL",toType = c("ENTREZID"),OrgDb = "org.Hs.eg.db")
cluster.go <- enrichGO(gene = cluster[,"ENTREZID"], keyType = "ENTREZID",OrgDb = 'org.Hs.eg.db',ont = "ALL",pAdjustMethod = "BH",pvalueCutoff = 0.01,qvalueCutoff = 0.05,readable = TRUE)
assign(paste0("cluster",j,".go"),cluster.go)
write.csv(cluster.go@result, file = paste0("cluster",j,"go",".csv"))
cluster.kegg <- enrichKEGG(gene = cluster[,"ENTREZID"],organism = 'hsa', pvalueCutoff = 0.05,pAdjustMethod = 'BH', minGSSize = 10,maxGSSize = 500,qvalueCutoff = 0.2,use_internal_data = FALSE)
assign(paste0("cluster",j,".kegg"),cluster.kegg)
write.csv(cluster.kegg@result, file = paste0("cluster",j,"kegg",".csv"))
write.csv(x = cluster.markers,file = paste0("cluster",j,".csv"))
}