Create scMetaLink Object

Initialize a scMetaLink object from expression data and cell metadata

createScMetaLink(
  expression_data,
  cell_meta,
  cell_type_column = "cell_type",
  min_cells = 10,
  min_genes = 200
)

Arguments

expression_data

A matrix or dgCMatrix of normalized expression values (genes x cells)

cell_meta

A data.frame containing cell metadata

cell_type_column

Character. Column name in cell_meta containing cell type annotations

min_cells

Integer. Minimum number of cells per cell type (default: 10)

min_genes

Integer. Minimum number of genes detected per cell (default: 200)

Value

A scMetaLink object

Examples

# \donttest{
# Create from expression matrix
expr_mat <- matrix(rpois(1000, 5), nrow = 100, ncol = 10)
rownames(expr_mat) <- paste0("Gene", 1:100)
colnames(expr_mat) <- paste0("Cell", 1:10)
meta <- data.frame(cell_type = rep(c("TypeA", "TypeB"), each = 5))
rownames(meta) <- colnames(expr_mat)
obj <- createScMetaLink(expr_mat, meta, "cell_type")
#> Error in createScMetaLink(expr_mat, meta, "cell_type"): No cell types with at least 10 cells
# }