• Ensembl, EntreID,Symbol这三种基因名格式的互相转换

#以人的12个基因(Symbol格式)为例
gene_symbol=c("RHO","CALM1","MEG3","GNGT1","SAG","RPGRIP1","TRPM1","PCP2","PCP4","AP1B1")

法1：org.Hs.eg.db包

library(org.Hs.eg.db)
keytypes(org.Hs.eg.db) 
gene_ids<-AnnotationDbi::select(org.Hs.eg.db, keys=as.character(gene_symbol), 
                  columns=c("ENSEMBL","ENTREZID"), #目标格式
                  keytype="SYMBOL") #目前的格式
gene_ids

gene_ids

library(org.Mm.eg.db)
keytypes(org.Mm.eg.db) 

法2：biomaRt包

library("biomaRt")
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
attributes = listAttributes(ensembl)
attributes[1:5,]
# library(httr)
# httr::set_config(config(ssl_verifypeer = 0L))
gene_ids2 <- getBM(filters= "hgnc_symbol", 
                    attributes= c("hgnc_symbol","ensembl_gene_id","entrezgene_id"),
                    values = gene_symbol, mart= ensembl)
gene_ids2

gene_ids2

• 将老鼠基因转为人类基因名

musGenes <- c("Hmmr", "Tlx3", "Cpeb4")

法1：直接转换

对于SYMBOL基因名格式，一般老鼠基因与人类基因就是大小写字母的区别。
人类基因名全部是大写，而老鼠基因名只有第一个字母是大写，其余为小写。

toupper(musGenes)
# [1] "HMMR"  "TLX3"  "CPEB4"

但也有例外，所以严谨点，可以使用下面的方法。

法2：biomaRt包

require("biomaRt")
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")

genes = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", 
                 values = musGenes, 
                 mart = mouse, 
                 attributesL = c("hgnc_symbol"), 
                 martL = human, uniqueRows=T)
#   MGI.symbol HGNC.symbol
# 1      Cpeb4       CPEB4
# 2       Hmmr        HMMR
# 3       Tlx3        TLX3