gene_id <- bitr(gene_symbol$SYMBOL, #前面得出的gene_symbol为数据框,所以这里要取子集 fromType = "SYMBOL", #需要转换的类型 toType = c("ENTREZID"), #需要转换为的类型 OrgDb = org.Hs.eg.db) #注释包 > head(gene_id) SYMBOL ENTREZID 1 MMP1 4312 2 CDC45 8318 3 NMU 10874 .. 4 ...
使用getBM函数将Entrez ID转换为基因Symbol: R dat <- getBM(attributes = c("entrezgene_id", "external_gene_name"), filters = "entrezgene_id", values = entrez_ids, mart = mart) 检查并返回转换结果: R print(dat) 这两种方法都可以有效地将Entrez ID转换为基因Symbol,你可以根据自己的...
③ Entrez ID转换为Gene symbol cc2 <- bitr(cc$`Gene ID`,fromType = 'ENTREZID',toType = 'SYMBOL',OrgDb = "org.Hs.eg.db") ④ Gene symbol转换为Entrez ID和Ensemble Gene ID cc2 <- bitr(cc$`Gene Symbol`,fromType = 'SYMBOL',toType = c("ENSEMBL","ENTREZID"),OrgDb = "org.Hs...
参考:基因 ID 和 Symbol 转换https://www.jianshu.com/p/7fde2fc6efa4 # 导入Homo_sapiens.gene_info 到 Rstudio,完成id转换gene_info=fread("Homo_sapiens.gene_info.cp",sep="\t")head(gene_info);dim(gene_info)# 75533 16names(gene_info)[1]"#tax_id"[2]"GeneID"[3]"Symbol"[4]"LocusT...
R语言ENTREZID ID 转换 gene SYMBOL library(data.table) library(org.Hs.eg.db) library(clusterProfiler) setwd("example") dt <- read.table("VanAllen.self_subtract", sep ="\t", header =T) dt$geneid<-rownames(dt)#transform idmap_dt <- bitr(dt$geneid, fromType ="ENTREZID",toType =...
R语言ENTREZID ID 转换 gene SYMBOL library(data.table) library(org.Hs.eg.db) library(clusterProfiler) setwd("example") dt <- read.table("VanAllen.self_subtract", sep ="\t", header =T) dt$geneid<-rownames(dt)#transform idmap_dt <- bitr(dt$geneid, fromType ="ENTREZID",toType =...
基因entrez ID转换 Gene Symbol 名字 R语言 setwd("/share/nas1/huangls/test/hypertension") library(org.Hs.eg.db) library(annotate) df=read.table("GPL19109.soft.1",header = T,sep = "\t",stringsAsFactors = F) df=df[!is.na(df$ENTREZ_GENE_ID),] ...
可以看到,都是ENTREZID,是不是不够直观?所以Y叔用了一个函数,setReadable,用一下神清气爽,ENTREZID转成symbol了。 kk2=setReadable(kk,OrgDb="org.Hs.eg.db",keyType="ENTREZID")head(kk2@result$geneID) ##[1]"CDC45/CDC20/CCNB2/CCNA2/CDK1/MAD2L1/TTK/CHEK1/CCNB1/MCM5/PTTG1"##[2]"CDC...
Ensembl Gene ID就是以E开头的一大长串的ID，一般从TCGA下载的数据多为这种ID，而Gene Symbol就是我们...