代码如下
DEG1 <- DEG_symbolid2
gene_up <- DEG1[DEG1$g == "up", "ENTREZID"]
gene_down <- DEG1[DEG1$g == "down","ENTREZID" ]
gene_diff <- c(gene_up,gene_down)
gene_all <- as.character(DEG1[,"ENTREZID"])
geneList <- DEG1$log2FoldChange
names(geneList)=DEG1$ENTREZID
geneList=sort(geneList,decreasing = T)
if(F){
go_enrich_results <- lapply( g_list , function(gene) {
lapply( c('BP','MF','CC') , function(ont) {
cat(paste('Now process ',ont ))
ego <- enrichGO(gene = gene,
universe = gene_all,
OrgDb = org.Hs.eg.db,
ont = ont ,
pAdjustMethod = "BH",
pvalueCutoff = 0.99,
qvalueCutoff = 0.99,
readable = TRUE)
print( head(ego) )
return(ego)
})
})
save(go_enrich_results,file = 'go_enrich_results.Rdata')
}
load(file = 'go_enrich_results.Rdata')
n1= c('gene_up','gene_down','gene_diff')
n2= c('BP','MF','CC')
for (i in 1:3){
for (j in 1:3){
fn=paste0('dotplot_',n1[i],'_',n2[j],'.png')
cat(paste0(fn,'\n'))
png(fn,res=150,width = 1080)
print( dotplot(go_enrich_results[[i]][[j]] ))
dev.off()
}
}
文章里面是做了生物过程和分析的两种分析。
