[英]convert Ensembl ID to gene name using biomaRt
我有一個名為kidney_ensembl
的數據集,我需要將 Ensembl ID 轉換為基因名稱。
我正在嘗試下面的代碼,但它不起作用。 有人可以幫助我嗎?
我知道有類似的問題,但他們沒有幫助我。 非常感謝!
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$gene_id
gene_IDs <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id","hgnc_symbol"),
values = genes, mart= mart)
kidney_final <- left_join(kidney, gene_IDs, by = NULL)
biomart 部分工作,它是你的左連接失敗,因為沒有公共列,gene_IDs 在“ensembl_gene_id”下有 ensembl id,而你的腎臟 dataframe 在“gene_id”下有它。
您還需要檢查它們是 gencode 還是 ensembl。 Gencode ids 通常有一個.[number] 例如,ENSG00000000003.10,在 ensembl 數據庫中它是 ENSG00000000003。
library("biomaRt")
library("dplyr")
kidney <- data.frame(gene_id =
c("ENSG00000000003.10","ENSG00000000005.5",
"ENSG00000000419.8","ENSG00000000457.9","ENSG00000000460.12"),
vals=runif(5)
)
#make this a character, otherwise it will throw errors with left_join
kidney$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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