Clean an expression matrix and collapse duplicated gene columns

Prepares a gene expression matrix for downstream analysis: drops unnamed and empty columns, expands columns with " /// " multi-mappings, maps gene identifiers when requested, and keeps the column with the largest median absolute deviation when several columns map to the same gene.

Usage

clean_expression(expression, id_from = NULL, id_to = "SYMBOL")

Arguments

expression: Numeric matrix or data frame with samples in rows and gene identifiers in columns.
id_from: Optional identifier type of the column names, for example "ENTREZID". When supplied, identifiers are translated to id_to with org.Hs.eg.db::org.Hs.eg.db, which must be installed.
id_to: Target identifier type used when id_from is supplied.

Value

A numeric matrix with samples in rows and unique gene identifiers in columns.

Examples

expr <- matrix(
  c(1, 2, 3, 4, 5, 6, NA, 8),
  nrow = 2,
  dimnames = list(NULL, c("A", "A", "B", ""))
)
clean_expression(expr)
#>      A B
#> [1,] 1 5
#> [2,] 2 6