利用biomaRt实现人鼠基因转换
2021-11-11 本文已影响0人
yingyonghui
library(biomaRt)
options(stringsAsFactors=F)
human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl")
mouse.genes <- read.table('color.signatures.txt',sep='\n',header=F)
geneset <- strsplit(mouse.genes[3,],split='\t')[[1]]
鼠-->人
genes.map = getLDS(mart=mouse, attributes=c("mgi_symbol"), filters="mgi_symbol", values=geneset[c(-1,-2)], attributesL=c("hgnc_symbol"), martL=human, uniqueRows=T)
write.table(genes.map,"mouse.to.human.genes.csv",row.names=F,col.names=T,quote=F)
clusterProfiler实现同一物种间不同gene名称之间的转换
library(org.Hs.eg.db)
library(clusterProfiler)
rm(list=ls())
geneset <- bitr(geneset, fromType="ENTREZID",toType=c( "SYMBOL"),OrgDb = org.Hs.eg.db)$SYMBOL
