R语言对基因进行GO注释（附代码）

通常在挑选出一些基因之后，需要对这些基因进行GO注释，分析该基因的功能，现在把R分析GO的代码放在下面

所需要的文件，有一列geneid即可

rm(list=ls())
genelist <- read.csv("C:/Users/Desktop/go.csv",header =TRUE)
library(AnnotationDbi)
BiocManager::install("org.Mm.eg.db",force = TRUE)
options(connectionObserver = NULL)
options(stringsAsFactors = F)
suppressMessages(library(org.Mm.eg.db))
library(org.Mm.eg.db)
genelist$symbol <- mapIds(org.Mm.eg.db,
                          keys=genelist$geneid, #这个geneid是跟你读取数据的列名一致
                          column="SYMBOL",
                          keytype="ENSEMBL",
                          multiVals="first")
genelist$entrez <- mapIds(org.Mm.eg.db,
                          keys=genelist$geneid,
                          column="ENTREZID",
                          keytype="ENSEMBL",
                          multiVals="first")

BiocManager::install("clusterProfiler",force = TRUE)
library(clusterProfiler)

erich.go.BP = enrichGO(gene = genelist$entrez,
                       
                       OrgDb = org.Mm.eg.db,
                       
                       keyType = "ENTREZID",
                       
                       pAdjustMethod = "BH",
                       
                       ont = "BP",
                       pvalueCutoff = 0.05,
                       qvalueCutoff = 0.05)
barplot(erich.go.BP) 
emapplot(erich.go.BP, showCategory = 30)

erich.go.CC = enrichGO(gene = genelist$entrez,
                       
                       OrgDb = org.Mm.eg.db,
                       
                       keyType = "ENTREZID",
                       
                       pAdjustMethod = "BH",
                       
                       ont = "CC",
                       pvalueCutoff = 0.05,
                       qvalueCutoff = 0.05)
barplot(erich.go.CC)
erich.go.MF = enrichGO(gene = genelist$entrez,
                       
                       OrgDb = org.Mm.eg.db,
                       
                       keyType = "ENTREZID",
                       
                       pAdjustMethod = "BH",
                       
                       ont = "MF",
                       pvalueCutoff = 0.05,
                       qvalueCutoff = 0.05)
barplot(erich.go.MF)
ALL <- enrichGO(gene=genelist$entrez,
                
                OrgDb=org.Mm.eg.db,
                
                keyType = "ENTREZID",
                
                ont = 'ALL',
                
                pAdjustMethod = "BH",
                
                pvalueCutoff = 0.05,
                qvalueCutoff = 0.05,
                readable = TRUE)  #readable = TRUE 这行代码可以使enrez转换为gene_symbol输出

library(ggplot2)
barplot(ALL, split="ONTOLOGY")+ facet_grid(ONTOLOGY~.,scale="free") 

#下面两行代码为画那个go注释网络图的
x2 <- pairwise_termsim(ALL)
emapplot(x2, showCategory = 30)
#存取所获取到的go注释的文件
ALLGO <- as.data.frame(ALL@result)
write.csv(as.data.frame(ALL@result), file="C:/Users/Desktop/2cellgo.csv",quote=FALSE)