Extract expression data and metadata from a Seurat object.
Usage
extract_seurat_data(
seurat_obj,
assay = "RNA",
cell_type_col = NULL,
output_dir = NULL,
prefix = "",
sparse = FALSE
)
Arguments
- seurat_obj
A Seurat object.
- assay
Assay to extract. Default is "RNA".
- cell_type_col
Column containing cell type labels.
- output_dir
Directory to save output files. If NULL, returns data.
- prefix
File name prefix for output files.
- sparse
Save expression as sparse matrix. Default is FALSE.
Value
If output_dir is NULL, returns a list. Otherwise saves files.
Examples
if (FALSE) { # \dontrun{
# Extract to files
extract_seurat_data(seurat_obj, "RNA", "celltype", "input/")
# Extract to R objects
data <- extract_seurat_data(seurat_obj, "RNA", "celltype")
} # }