- scvi.data.read_h5ad(filename, backed=None, *, as_sparse=(), as_sparse_fmt=<class 'scipy.sparse._csr.csr_matrix'>, chunk_size=6000)#
Read .h5ad-formatted hdf5 file.
If ‘r’, load
AnnDatain backed mode instead of fully loading it into memory (memory mode). If you want to modify backed attributes of the AnnData object, you need to choose ‘r+’.
Currently, backed only support updates to X. That means any changes to other slots like obs will not be written to disk in backed mode. If you would like save changes made to these slots of a backed
AnnData, write them to a new file (see
write()). For an example, see [here] (https://anndata-tutorials.readthedocs.io/en/latest/getting-started.html#Partial-reading-of-large-data).
6000)) – Used only when loading sparse dataset that is stored as dense. Loading iterates through chunks of the dataset of this row size until it reads the whole dataset. Higher size means higher memory consumption and higher (to a point) loading speed.
- Return type