h5seurat_to_anndata: Convert: 'h5Seurat' ==> 'anndata'

In bschilder/scKirby: Automated ingestion and conversion of various single-cell data formats.

Convert: h5Seurat ==> anndata

Description

Convert: h5Seurat ==> anndata

Usage

h5seurat_to_anndata(
  obj,
  reimport = TRUE,
  save_path = tempfile(fileext = ".h5ad"),
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

Arguments

obj	A single-cell object supported by scKirby. See converters for a table of all supported conversions.
reimport	Save and re-import the AnnData object into R to ensure all data has been converted from Python-native to R-native objects (e.g. pandas data.frames vs. R data.frames).
save_path	Path to save the H5Seurat to.
overwrite	Overwrite existing dest
verbose	Print messages.
...	Arguments passed on to anndata::write_h5ad anndata An AnnData() object filename Filename of data file. Defaults to backing file. compression See the h5py filter pipeline. Options are "gzip", "lzf" or NULL. compression_opts See the h5py filter pipeline. as_dense Sparse in AnnData object to write as dense. Currently only supports "X" and "raw/X".

Examples

obj <- example_obj("h5seurat")
obj2 <- h5seurat_to_anndata(obj)

bschilder/scKirby documentation built on April 22, 2024, 12:13 a.m.