1.同物種ID的轉(zhuǎn)換

Gene id 轉(zhuǎn)換(四種基因各種id轉(zhuǎn)換方法)_易易歡歡的博客-CSDN博客_gene id轉(zhuǎn)換

library("clusterProfiler")
library("org.Hs.eg.db")
gene.df <- bitr(gene, fromType = "ENTREZID", 
                toType = c("ENSEMBL", "SYMBOL"), 
                OrgDb = org.Hs.eg.db)#Orgdb是指對應(yīng)的注釋包是哪個
head(gene.df)

geneid <- AnnotationDbi::select(
    org.Hs.eg.db, keys=gene, keytype="SYMBOL", columns=c("ENTREZID","ENSEMBL")
)

gene <-AnnotationDbi::mapIds(org.Hs.eg.db, 
                      keys=gene,
                      column="SYMBOL", 
                      keytype="ENTREZID")#

library(AnnotationDbi)
mySymbols <- AnnotationDbi::mget(gene,
                  org.Hs.egSYMBOL,
                  ifnotfound=NA)

曾老師給大家的福利，能夠轉(zhuǎn)換各種探針名字
jmzeng1314/AnnoProbe (github.com)

ibrary(devtools)
install_github("jmzeng1314/AnnoProbe")
library(AnnoProbe)

使用biomaRt和gtf進行轉(zhuǎn)換ID

轉(zhuǎn)錄組完整的ID轉(zhuǎn)換：biomaRt和gtf - 簡書 (jianshu.com)

library(rtracklayer)
gff <- readGFF("genes.gtf")
mapid <- gff[gff$type == "gene", c("gene_id", "gene_name")]
# 用merge進行合并
S1name=data.frame(geneid=data$gene)
dim(df)
df <- merge(S1name, mapid, by.x="geneid", by.y="gene_name")

2.不同物種ID的轉(zhuǎn)換

biomaRt包實現(xiàn)不同物種之間同源基因轉(zhuǎn)換 - 騰訊云開發(fā)者社區(qū)-騰訊云 (tencent.com)

https://mp.weixin.qq.com/s/FKAXJecDT_rcrrbTtjeQQw

library(biomaRt)
human <- useMart('ensembl',dataset = "hsapiens_gene_ensembl")
mouse <- useMart('ensembl',dataset = "mmusculus_gene_ensembl")
m2h.g <- getLDS(attributes = c("mgi_symbol"),filters = "mgi_symbol",
       values = mouse.gene,mart = mouse,
       attributesL = c("hgnc_symbol","chromosome_name","start_position"),
       martL = human,uniqueRows = T)

如何快速查找物種間對應(yīng)的同源基因 - 知乎 (zhihu.com)

#安裝homologene這個R包
install.packages('homologene')
#加載homologene這個R包
library(homologene)
#這里以小鼠的三個基因為例
#更多基因方法是一樣的
genelist<-c("Acadm","Eno2","Acadvl")
#使用homologene函進行轉(zhuǎn)換
#@genelist是要轉(zhuǎn)換的基因列表
#@inTax是輸入的基因列表所屬的物種號，10090是小鼠
#@outTax是要轉(zhuǎn)換成的物種號，9606是人
homologene(genelist, inTax = 10090, outTax = 9606)