Extract expression matrix from Seurat object

Extract expression data from a Seurat object, compatible with both V4 and V5.

Usage

extract_expression(
  seurat,
  layer = c("data", "counts", "scale.data"),
  assay = "RNA",
  as_dense = FALSE
)

Arguments

seurat

Seurat object

layer

Layer/slot to extract: "counts", "data" (normalized), or "scale.data"

assay

Assay name (default: "RNA")

as_dense

Convert to dense matrix (default: FALSE)

Value

Expression matrix (genes x cells)

Examples

if (FALSE) { # \dontrun{
# Get normalized expression
expr <- extract_expression(seurat, layer = "data")

# Get raw counts as dense matrix
counts <- extract_expression(seurat, layer = "counts", as_dense = TRUE)
} # }