I have a dataset called kidney_ensembl and I need to convert Ensembl IDs to gene names.
I'm trying the code below, but it's not working. Can somebody help me?
I know there are similar questions, but they are not helping me. Many thanks!
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$gene_id
gene_IDs <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id","hgnc_symbol"),
values = genes, mart= mart)
kidney_final <- left_join(kidney, gene_IDs, by = NULL)
The biomart part worked, it's your left join that fails because there are no common columns, gene_IDs has the ensembl id under "ensembl_gene_id" while your kidney dataframe has it under "gene_id".
Also you need to check whether they are gencode or ensembl. Gencode ids normally have a .[number] for example, ENSG00000000003.10 , in ensembl database it is ENSG00000000003.
library("biomaRt")
library("dplyr")
kidney <- data.frame(gene_id =
c("ENSG00000000003.10","ENSG00000000005.5",
"ENSG00000000419.8","ENSG00000000457.9","ENSG00000000460.12"),
vals=runif(5)
)
#make this a character, otherwise it will throw errors with left_join
kidney$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