Converts an AnnData zarr store to h5seurat format, translating AnnData conventions (categories/codes 0-based, cells x genes CSR, obsm arrays) to h5seurat layout (levels/values 1-based, genes x cells CSC, reductions/cell.embeddings). By default uses streaming that avoids a Seurat intermediate.
Usage
ZarrToH5Seurat(
source,
dest,
assay = "RNA",
overwrite = FALSE,
gzip = 4L,
verbose = TRUE,
stream = TRUE
)Arguments
- source
Path to input .zarr directory
- dest
Path for output .h5seurat file
- assay
Assay name (default "RNA")
- overwrite
If TRUE, overwrite existing output
- gzip
Gzip compression level (0-9)
- verbose
Show progress messages
- stream
If TRUE (default), stream fields directly. If FALSE, load as Seurat then save as h5seurat.