Create Single-Cell PhyloExpressionSet from Expression Matrix

Create a ScPhyloExpressionSet object from an expression matrix and metadata.

Usage

ScPhyloExpressionSet_from_matrix(
  expression_matrix,
  strata,
  metadata,
  groups_column = NULL,
  name = "Single-Cell Phylo Expression Set",
  ...
)

Arguments

expression_matrix

Sparse or dense expression matrix with genes as rows and cells as columns

strata

Factor vector of phylostratum assignments for each gene

metadata

Data frame with cell metadata, rownames should match colnames of expression_matrix

groups_column

Character string specifying which metadata column to use for initial grouping (default: first factor column found)

name

A character string naming the dataset (default: "Single-Cell Phylo Expression Set")

...

Additional arguments passed to ScPhyloExpressionSet constructor

Value

A ScPhyloExpressionSet object

Details

This function creates a ScPhyloExpressionSet from basic components. The groups_column parameter determines the initial selected_idents value, which can be changed later using the setter. All discrete columns in metadata are automatically converted to factors for consistent handling.

Examples

if (FALSE) { # \dontrun{
# Create from matrix and metadata
sc_set <- ScPhyloExpressionSet_from_matrix(expr_matrix, strata, metadata,
                                          groups_column = "cell_type")

# Later change grouping
sc_set@selected_idents <- "treatment_group"
} # }