I have 10x scRNA-seq data for a dog. The genes are in ensembl id format. I converted them to gene symbols using biomaRt and added to the Seurat features metadata like this:
HCC1@assays$RNA@meta.features <- merge(HCC1@assays$RNA@meta.features, gfile, by=0, all.x=TRUE)
So my HCC1@assays$RNA@meta.features looks like this
The reason why I do not want to convert features into gene symbols right away is that there are many duplicate gene symbols after conversion. That is why I want to use gene symbols in the end for annotation only.
However, for quality control purposes I need gene names (to find percentages of mitochondrial and ribosomal genes).
Is there a way to refer to the gene names when using PercentageFeatureSet? For example in this line:
HCC1[["percent.rb"]] <- PercentageFeatureSet(HCC1, pattern="^MT-")