Standardize gene symbols in a count matrix or Seurat object

This function helps unify gene symbols to a standard format. It can:

1. Convert gene IDs to gene symbols (if is_gene_id = TRUE).

2. Check and correct gene symbols using HGNChelper::checkGeneSymbols.

3. Aggregate duplicated gene symbols by summing their counts.

Usage

sn_standardize_gene_symbols(x, species = NULL, is_gene_id = FALSE)

Arguments

x

A count matrix or a Seurat object.

species

The species for gene symbol checking, passed to HGNChelper.

is_gene_id

If TRUE, x is assumed to contain gene IDs (e.g., ENSEMBL IDs) as rownames.

Value

If x is a matrix, returns a matrix with standardized gene symbols. If x is a Seurat object, returns the modified Seurat object.

Examples

if (FALSE) { # \dontrun{
# For a Seurat object:
seurat_obj <- sn_standardize_gene_symbols(seurat_obj, species = "human", is_gene_id = FALSE)

# For a matrix:
counts_mat <- sn_standardize_gene_symbols(counts_mat, species = "human", is_gene_id = TRUE)
} # }