Adding column of gene symbol in a count matrix with ensemble ID names Seurat object .RDS file

Question

I am trying to carry out a single-cell analysis in which I started with a .RDS file. I was developing the workflow but I have stopped in the Quality control, because I need to add de "percent.mt" column in the count matrix of the dataset. I was trying but I discovered that the genes was named by ENSEMBLE ID nomenclature, and I need it in genesymbol. While trying to add that column, I found an error in the last step of it. I will show my script in case somebody could help me! Thank you in advance.

Upload .RDS file

bonemarrow \<- readRDS(file = "C:/Users/merce/Documents/Máster en Bioinformática/TFM/be8db92e-e52c-430c-b3d1-c27b506f8c2e.rds")
str(bonemarrow)
slotNames(bonemarrow)
View([email protected])

Extract the expression count array from the Seurat object.

In this code, pbmc.data1@assays$RNA@counts accesses the expression count matrix inside the Seurat object pbmc.data1. Then, this count array is passed as counts argument to CreateSeuratObject

counts_matrix <- bonemarrow@assays$RNA@counts

Create a new Seurat object using the extracted counts matrix:

bonecounts<- CreateSeuratObject(counts = counts_matrix, project = "seuratM")
bonecounts

Quality control (QCONTROL):

View([email protected])

#1. PERCENT-MT

# calculate the percentage of mt

# Calculate the percentage of mitochondrial gene expression and assign it to the Seurat object.

# You can get the Ensembl IDs of the rows of the counts matrix.

ensembl_ids \<- rownames(counts_matrix)

Load the genomic annotation database for Mus musculus

if (!requireNamespace("org.Mm.eg.db", quietly = TRUE)) {
    install.packages("org.Mm.eg.db")
}
library(org.Mm.Mm.eg.db)

Get the gene symbols corresponding to the Ensembl IDs

gene_symbols \<- select(org.Mm.eg.db, keys=ensembl_ids, columns="SYMBOL", keytype="ENSEMBL")

Now, gene_symbols contains a mapping between Ensembl IDs and gene symbols.

You can add the gene symbols to your count matrix as row names

*rownames(counts_matrix) \<- gene_symbols$SYMBOL*

At this step, I found this error:

rownames(counts_matrix) <- gene_info$external_gene_name
Error in fixupDN.if.valid(value, x@Dim) :
length of Dimnames[[1]] (17982) is not equal to Dim[1] (17985)