Stream a sparse matrix group from one HDF5 file to another — .stream_sparse

Copies data/indices/indptr arrays with optional CSR<->CSC reinterpretation. CSR of [A x B] has identical on-disk layout to CSC of [B x A], so conversion between h5ad CSR (cells x genes) and h5seurat CSC (genes x cells) requires only swapping the shape/dims attribute.

Usage

.stream_sparse_group(
  src_group,
  dst_parent,
  dst_name,
  gzip,
  src_format = "h5ad",
  dst_format = "h5seurat",
  assay = NULL
)

Arguments

src_group: H5Group containing data/indices/indptr
dst_parent: H5Group to write into
dst_name: Name for new group in dst_parent
gzip: Integer gzip compression level
src_format: Character, "h5ad" or "h5seurat" or "h5mu"
dst_format: Character, "h5ad" or "h5seurat"
assay: Character assay name (for h5seurat graphs)