Read or write a sparse matrix from an anndata hdf5 file. These functions will
automatically transpose matrices when converting to/from the AnnData
format. This is because the AnnData convention stores cells as rows, whereas the R
convention stores cells as columns. If this behavior is undesired, call t()
manually on the matrix inputs and outputs of these functions.
Usage
open_matrix_anndata_hdf5(path, group = "X", buffer_size = 16384L)
write_matrix_anndata_hdf5(
mat,
path,
group = "X",
buffer_size = 16384L,
chunk_size = 1024L,
gzip_level = 0L
)Arguments
- path
Path to the hdf5 file on disk
- group
The group within the hdf5 file to write the data to. If writing to an existing hdf5 file this group must not already be in use
- buffer_size
For performance tuning only. The number of items to be buffered in memory before calling writes to disk.
- chunk_size
For performance tuning only. The chunk size used for the HDF5 array storage.
- gzip_level
Gzip compression level. Default is 0 (no compression)
