代碼如下，謝謝指導(dǎo)
DEG_symbolid2$g <- ifelse(DEG_symbolid2$pvalue > 0.05, "stable",
ifelse(DEG_symbolid2$log2FoldChange > logFC_t,"up",
ifelse(DEG_symbolid2$log2FoldChange <logFC_t,"down","stable")))
DEG1 <- DEG_symbolid2
gene_up <- DEG1[DEG1$g == "up", "entrezgene_id"]
gene_down <- DEG1[DEG1$g == "down","entrezgene_id" ]
gene_diff <- c(gene_up,gene_down)
gene_all <- as.character(DEG1[,"entrezgene_id"])
geneList <- DEG1$log2FoldChange
names(geneList)=DEG1$entrezgene_id
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()
}
}
input：
dotplot_gene_diff_BP.png
dotplot_gene_diff_CC.png
dotplot_gene_diff_MF.png
生物學(xué)意義：BP,CC,MF
這些挑選出來的差異化基因主要是富集在哪些通路上。
KEGG通路
kk_gse <- gseKEGG(geneList = geneList,
organism = 'hsa',
nPerm = 1000,
minGSSize = 120,
pvalueCutoff = 0.9,
verbose = FALSE)
head(kk_gse)[,1:6]
emapplot(kk_gse, showCategory = 100)
cnetplot(kk_gse, showCategory = 5)
input：
image.png
image.png
謝謝指導(dǎo)
代碼參考生信技能樹，感謝
