Convert Expression Matrix Between Species

Applies species conversion mapping to an expression matrix, handling one-to-many gene mappings with specified aggregation method.

Usage

convert_expression_matrix(
  expr_matrix,
  gene_mapping,
  handle_duplicates = c("mean", "sum", "max")
)

Arguments

expr_matrix

Matrix or data.frame. Expression data (genes x cells/samples)

gene_mapping

Data.frame. Output from convert_species_biomart()$mapping

handle_duplicates

Character. Method for aggregating expression when multiple source genes map to one target gene:

• "mean": Average expression (default, conservative)

• "sum": Sum expression (appropriate for count data)

• "max": Maximum expression

Value

List with elements:

• expr_matrix: Converted expression matrix (target genes x cells)

• conversion_info: data.frame with mapping details

• stats: list with conversion statistics

Examples

if (FALSE) { # \dontrun{
# After obtaining mapping
mapping_result <- convert_species_biomart(
  genes = rownames(mouse_expr),
  from_species = "Mus_musculus"
)

# Convert expression matrix
converted <- convert_expression_matrix(
  expr_matrix = mouse_expr,
  gene_mapping = mapping_result$mapping,
  handle_duplicates = "mean"
)

# Use converted matrix
human_expr <- converted$expr_matrix
} # }