Convert ensemble genes to gene names in my sigle cell signature matrix annotated with seurat in R?

Question

I have single cell data which I want to annotate with the seurat package, so I ran this code in R:

lung.data <- Read10X(data.dir ="C:/Users/Desktop/SINGLE-CELL/DATA",gene.column = 1)

lung <- CreateSeuratObject(counts = lung.data, project = "lung", min.cells = 3, min.features = 200)

And the output of the features of this seurat object is:

    >rownames(lung)
    [1] "ENSG00000000003" "ENSG00000000419"
 [3] "ENSG00000000457" "ENSG00000000460"
 [5] "ENSG00000000938" "ENSG00000000971"
 [7] "ENSG00000001036" "ENSG00000001084"
 [9] "ENSG00000001167" "ENSG00000001460"
[11] "ENSG00000001461" "ENSG00000001497"
[13] "ENSG00000001561" "ENSG00000001617"
[15] "ENSG00000001626" "ENSG00000001629"
[17] "ENSG00000001630" "ENSG00000001631"
[19] "ENSG00000002016" "ENSG00000002079"

How can I change the row names of this Seurat Object from Ensembl to gene name, knowing that not all the ensemble genes have conversion to gene name, in order to obtain the seurat object with the gene names as row names and cell names as column names?

Answer 1

From Seurat developers:

the functions Read10X has an argument gene.column that can be used to change between using the gene name and the ensembl ID when reading in 10x Genomics datasets. You can also use the use.names parameter when using Read10X_h5."

Answer 2

I think BioMart will do the gene ID -> gene name conversion you're after: https://www.ensembl.org/info/data/biomart/index.html

To use BioMart to convert the gene IDs to gene names, you can use the BioMaRt bioconductor R package. Installation and running instructions can be found here: ensembl.org/info/data/biomart/biomart_r_package.html

For this query, you will need to use the human genes dataset:

ensembl = useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl")

Then use your list of gene IDs as the 'Filter', with list of IDs as the values:

filters = 'ensembl_gene_id' 

Most human protein-coding genes have an associated HGNC symbol, and these are used in Ensembl. Therefore, you can select the 'gene_name' attribute to retrieve the human gene names, and this will usually correspond to the HGNC gene names, as stored in the Ensembl database.

More information on gene names can be found in the Ensembl documentation: https://ensembl.org/info/genome/genebuild/gene_names.html