Convert an AnnData to an ZarrAnnData

Convert another AnnData object to an ZarrAnnData object

Usage

as_ZarrAnnData(
  adata,
  file,
  compression = c("none", "gzip", "blosc", "zstd", "lzma", "bz2", "zlib", "lz4"),
  mode = c("w-", "r", "r+", "a", "w", "x"),
  zarr_format = NULL
)

Arguments

adata

An AnnData object to be converted to ZarrAnnData

file

The file name (character) of the .zarr file

compression

The compression algorithm to use when writing the Zarr file. Can be one of "none", "gzip", "blosc", "zstd", "lzma", "bz2", "zlib" or "lz4". Defaults to "none".

mode

The mode to open the Zarr file:

• a creates a new file or opens an existing one for read/write

• r opens an existing file for reading

• r+ opens an existing file for read/write

• w creates a file, truncating any existing ones

• w-/x are synonyms, creating a file and failing if it already exists

zarr_format

The format to use when creating the Zarr store. Should be either 2 or 3 for Zarr v2 or v3 formats, respectively. The default can also be set using the anndataR.zarr_format option, e.g. options(anndataR.zarr_format = 2). If neither is set, Zarr v3 is used.

When an existing store is opened, that store's format is used instead and setting zarr_format to a different format is an error. Use mode = "w" to rewrite an existing store in another format.

Value

A ZarrAnnData object with the same data as the input AnnData object.

See also

Other object converters: as_AnnData(), as_HDF5AnnData(), as_InMemoryAnnData(), as_ReticulateAnnData(), as_Seurat(), as_SingleCellExperiment(), reticulate-helpers