seurat2duckdb — seurat2duckdb • scSpotlight

Convert seurat object to onDisk duckdb file

Usage

seurat2duckdb(
  object,
  dbFile = "output.duckdb",
  assays = "RNA",
  layers = c("counts", "data"),
  reductions = Reductions(object),
  memory_limit = "4GB",
  threads = "8",
  overwrite = TRUE
)

Arguments

object: seurat object
dbFile: output duckdb filename, please ensure no previous db exists, connection will be closed after conversion
layers: layers to be converted, please ensure at least one of c("counts", "data") exists, scale.data is not supported yet
reductions: object reductions to be included, default: c("pca", "umap", "tsne")
memory_limit: memory limit for duckdb (SET memory_limit = '4GB';),
threads: threads used by duckdb driver, note: need to parse string here
overwrite: whether to overwrite existing tables, only could be TRUE for now
assay: searat assay used

Examples

if (FALSE) { # \dontrun{
pbmc <- LoadSeurat("pbmc3k.Rds")
seurat2duckdb(object = pbmc, dbFile = "pbmc3k.duckdb")
} # }