Match Expression Matrix with Phylostratum Map — match_map_sc

Join single-cell gene expression matrix with a phylostratum mapping to create a ScPhyloExpressionSet object.

Usage

match_map_sc_matrix(
  expression_matrix,
  metadata,
  phylomap,
  strata_legend = NULL,
  ...
)

Arguments

expression_matrix: Expression matrix with genes as rows and cells as columns
metadata: Data frame with cell metadata, rownames should match colnames of expression_matrix
phylomap: A data frame with two columns: phylostratum assignments and gene IDs
strata_legend: A data frame with two columns: phylostratum assignments and name of each stratum. If NULL, numeric labels will be used (default: NULL)
...: Additional arguments passed to ScPhyloExpressionSet_from_matrix

Value

A ScPhyloExpressionSet object

Details

This function combines phylostratum mapping with expression matrix and metadata to create a ScPhyloExpressionSet. Only genes present in both the expression matrix and phylomap will be retained. All discrete metadata columns are converted to factors automatically.

Examples

if (FALSE) { # \dontrun{
# Match expression matrix with phylostratum map
sc_set <- match_map_sc_matrix(expr_matrix, metadata, phylo_map)
} # }