[英]convert Ensembl ID to gene name using biomaRt
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,但他们没有帮助我。 非常感谢!
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$gene_id
gene_IDs <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id","hgnc_symbol"),
values = genes, mart= mart)
kidney_final <- left_join(kidney, gene_IDs, by = NULL)
biomart 部分工作,它是你的左连接失败,因为没有公共列,gene_IDs 在“ensembl_gene_id”下有 ensembl id,而你的肾脏 dataframe 在“gene_id”下有它。
您还需要检查它们是 gencode 还是 ensembl。 Gencode ids 通常有一个.[number] 例如,ENSG00000000003.10,在 ensembl 数据库中它是 ENSG00000000003。
library("biomaRt")
library("dplyr")
kidney <- data.frame(gene_id =
c("ENSG00000000003.10","ENSG00000000005.5",
"ENSG00000000419.8","ENSG00000000457.9","ENSG00000000460.12"),
vals=runif(5)
)
#make this a character, otherwise it will throw errors with left_join
kidney$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
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