使用 biomaRt 将 Ensembl ID 转换为基因名称

Question

我有一个名为 kidney_ensembl 的数据集，我需要将 Ensembl ID 转换为基因名称。

我正在尝试下面的代码，但它不起作用。有人可以帮助我吗？

我知道有类似的问题，但它们对我没有帮助。非常感谢！

converting from Ensembl gene ID's to different identifier

How can I convert Ensembl ID to gene symbol in R?

library(tidyverse)
kidney <- data.frame(gene_id = c("ENSG00000000003.10","ENSG00000000005.5",
"ENSG00000000419.8","ENSG00000000457.9","ENSG00000000460.12")
)
#kidney <- read_delim("Desktop/kidney_ensembl.txt", delim = "\t")

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

library("biomaRt")

mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
genes <-  kidney$gene_id
gene_IDs <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id","hgnc_symbol"),
              values = genes, mart= mart)

kidney_final <- left_join(kidney, gene_IDs, by = NULL)

Answer 1

biomart 部分起作用了，因为没有公共列，所以您的左连接失败了，gene_IDs 在“ensembl_gene_id”下有集成 id，而您的肾脏数据框在“gene_id”下有它。

您还需要检查它们是 gencode 还是 ensembl。 Gencode ids 通常有一个 .[number] 例如，ENSG00000000003.10，在 ensembl 数据库中它是 ENSG00000000003。

library("biomaRt")
library("dplyr")

kidney <- data.frame(gene_id = 
c("ENSG00000000003.10","ENSG00000000005.5",
"ENSG00000000419.8","ENSG00000000457.9","ENSG00000000460.12"),
vals=runif(5)
)
#make this a character, otherwise it will throw errors with left_join
kidney$gene_id <- as.character(kidney$gene_id)
# in case it's gencode, this mostly works
#if ensembl, will leave it alone
kidney$gene_id <- sub("[.][0-9]*","",kidney$gene_id)

mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
genes <-  kidney$gene_id
gene_IDs <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id","hgnc_symbol"),
              values = genes, mart= mart)

left_join(kidney, gene_IDs, by = c("gene_id"="ensembl_gene_id"))

          gene_id      vals hgnc_symbol
1 ENSG00000000003 0.2298255      TSPAN6
2 ENSG00000000005 0.4662570        TNMD
3 ENSG00000000419 0.7279107        DPM1
4 ENSG00000000457 0.3240166       SCYL3
5 ENSG00000000460 0.3038986    C1orf112