anndataR: AnnData interoperability in R

An AnnData object. This class can either be an in-memory AnnData (InMemoryAnnData) or an HDF5-backed AnnData (HDF5AnnData). The AnnData object stores a data matrix X together with annotations of observations obs (obsm, obsp) and variables var (varm, varp). Additional layers of data can be stored in layers and unstructured annotations in uns.

Functions that can be used to create AnnData objects

• AnnData(): Create an in-memory AnnData object.

• read_h5ad(): Read an HDF5-backed AnnData file from disk.

• from_SingleCellExperiment(): Convert a SingleCellExperiment object to an AnnData object.

• from_Seurat(): Convert a Seurat object to an AnnData object.

An AnnData object has the following slots

Access them by using the $ operator. Example: adata$obs.

• X: A matrix of observations by variables.

• obs: A data frame of observations.

• var: A data frame of variables.

• obs_names: Names of observations (alias for rownames(obs)).

• var_names: Names of variables (alias for rownames(var)).

• layers: A named list of matrices with the same dimensions as X.

• obsm: A named list of matrices with the same number of rows as obs.

• varm: A named list of matrices with the same number of rows as var.

• obsp: A named list of sparse matrices with the same number of rows and columns as the number of observations.

• varp: A named list of sparse matrices with the same number of rows and columns as the number of variables.

• uns: A named list of unstructured annotations.

An AnnData object has the following methods

Access them by using the $ operator. Example: adata$write_h5ad().

• print(): Print a summary of the AnnData object.

• shape(): Dimensions (observations x variables) of the AnnData object.

• n_obs(): Number of observations in the AnnData object.

• n_vars(): Number of variables in the AnnData object.

• obs_keys(): Column names of obs.

• var_keys(): Column names of var.

• layers_keys(): Element names of layers.

• obsm_keys(): Element names of obsm.

• varm_keys(): Element names of varm.

• obsp_keys(): Element names of obsp.

• varp_keys(): Element names of varp.

• uns_keys(): Element names of uns.

• write_h5ad(): Write the AnnData object to an HDF5 file.

Conversion methods

Access them by using the $ operator. Example: adata$to_Seurat().

• to_SingleCellExperiment(): Convert to SingleCellExperiment.

• to_Seurat(): Convert to Seurat.

• to_InMemoryAnnData(): Convert to an InMemory AnnData.

• to_HDF5AnnData(): Convert to an HDF5 Backed AnnData.

See also

Useful links:

• https://scverse.org/anndataR

• https://github.com/scverse/anndataR

• Report bugs at https://github.com/scverse/anndataR/issues

Author

Maintainer: Robrecht Cannoodt robrecht@data-intuitive.com (ORCID) (rcannood)

Authors:

• Luke Zappia luke@lazappi.id.au (ORCID) (lazappi)

• Martin Morgan mtmorgan.bioc@gmail.com (ORCID) (mtmorgan)

• Louise Deconinck louise.deconinck@gmail.com (ORCID) (LouiseDck)

Other contributors:

• Danila Bredikhin danila.bredikhin@embl.de (ORCID) (gtca) [contributor]

• Isaac Virshup (ORCID) (ivirshup) [contributor]

• Brian Schilder brian_schilder@alumni.brown.edu (ORCID) (bschilder) [contributor]

• Chananchida Sang-aram (ORCID) (csangara) [contributor]

• Data Intuitive info@data-intuitive.com [funder, copyright holder]

• Chan Zuckerberg Initiative [funder]