Save a Seurat object as an anndata h5ad file

Usage

SeuratToAnnData(
  object,
  outFile = NULL,
  main.assay = "RNA",
  main.layer = "counts",
  transfer.other.main.layers = NULL,
  transfer.other.assays.layers = NULL,
  transfer.graphs = TRUE
)

Arguments

object: Seurat object
outFile: Name of the target file to write the anndata object
main.assay: Assay to transfer to AnnData as X
main.layer: Layer to transfer to AnnData as X
transfer.other.main.layers: Which other layers to transfer into AnnData
transfer.other.assays.layers: Which other assay-layer pairs to transfer into AnnData (since AnnData only takes one assay for now)
transfer.graphs: Whether to transfer Graphs to AnnData .uns

Value

Writes a Seurat object to an .h5ad file after anndata conversion

References

Code adapted from the awesome sceasy github!