snapatac2.AnnDataSet

class snapatac2.AnnDataSet(*, adatas, filename, add_key)

Similar to AnnData, AnnDataSet contains annotations of observations obs (obsm, obsp), variables var (varm, varp), and unstructured annotations uns. Additionally it provides lazy access to concatenated component AnnData objects, including X, obs, obsm, obsp.

Parameters

• adatas (list[(str, Path)] | list[(str, AnnData)]) – List of key and file name (or backed AnnData object) pairs.

• filename (Path) – File name of the output file containing the AnnDataSet object.

• add_key (str) – The column name in obs to store the keys

Note

AnnDataSet does not copy underlying AnnData objects. It stores the references to individual anndata files. If you move the anndata files to a new location, remember to update the anndata file locations when opening an AnnDataSet object.

See also

read_dataset

Attributes

X	Vertically concatenated data matrices of shape n_obs x n_vars.
adatas	View into the component AnnData objects.
isbacked	Whether the AnnDataSet object is backed.
n_obs	Number of observations.
n_vars	Number of variables/features.
obs	One-dimensional annotation.
obs_names	Names of observations.
obsm	PyAxisArrays.
obsp	PyAxisArrays.
shape	Shape of data matrix (n_obs, n_vars).
uns	Unstructured annotation (ordered dictionary).
var	One-dimensional annotation.
var_names	Names of variables.
varm	PyAxisArrays.
varp	PyAxisArrays.

Methods

chunked_X(chunk_size, /)	Return an iterator over the rows of the data matrix X.
close()	Close the AnnDataSet object.
copy(dirname)	Copy the AnnDataSet object to a new location.
is_closed()	If the AnnDataSet object has been closed.
obs_ix(names)
subset(obs_indices, var_indices, out)	Subsetting the AnnDataSet object.
to_adata(file, copy_X, /)	Convert the AnnDataSet object to an AnnData object.
var_ix(names)