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

Question

I have a data.frame containing Ensembl IDs in one column; I would like to find corresponding gene symbols for the values of that column and add them to a new column in my da

Answer 1

I tried several R packages (mygene, org.Hs.eg.db, biomaRt, EnsDb.Hsapiens.v79) to convert Ensembl.gene to gene.symbol, and found that the EnsDb.Hsapiens.v79 package / gene database provides the best conversion quality (in terms of being able to convert most of Ensembl.gene to gene.symbol).

Install the package if you have not installed by running this command: BiocManager::install("EnsDb.Hsapiens.v79")

library(EnsDb.Hsapiens.v79)

# 1. Convert from ensembl.gene to gene.symbol
ensembl.genes <- c("ENSG00000150676", "ENSG00000099308", "ENSG00000142676", "ENSG00000180776", "ENSG00000108848", "ENSG00000277370", "ENSG00000103811", "ENSG00000101473")

geneIDs1 <- ensembldb::select(EnsDb.Hsapiens.v79, keys= ensembl.genes, keytype = "GENEID", columns = c("SYMBOL","GENEID"))

# 2. Convert from gene.symbol to ensembl.gene
geneSymbols <-  c('DDX26B','CCDC83',  'MAST3', 'RPL11', 'ZDHHC20',  'LUC7L3',  'SNORD49A',  'CTSH', 'ACOT8')

geneIDs2 <- ensembldb::select(EnsDb.Hsapiens.v79, keys= geneSymbols, keytype = "SYMBOL", columns = c("SYMBOL","GENEID"))

Other available R packages / gene database for the conversion can refer to this GitHub page.

My answer to similar question in bioinformatics.stackexchange.

Answer 2

This is because the values you have in your gene column are not gene ids, they are peptide id (they start with ENSP). To get the info you need, try replacing ensembl_gene_id by ensembl_peptide_id:

G_list <- getBM(filters = "ensembl_peptide_id", 
                attributes = c("ensembl_peptide_id", "entrezgene", "description"),
                values = genes, mart = mart)

Also, what you are really looking for is the hgnc_symbol

Here is the total code to get your output:

library('biomaRt')
mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
genes <- df$genes
df<-df[,-4]
G_list <- getBM(filters= "ensembl_peptide_id", attributes= c("ensembl_peptide_id","hgnc_symbol"),values=genes,mart= mart)
merge(df,G_list,by.x="gene",by.y="ensembl_peptide_id")