episcanpy.api.ct.save_sparse_mtx

episcanpy.api.ct.save_sparse_mtx(initial_matrix, output_file='.h5ad', path='', omic='ATAC', bed=False, save=True)

Convert regular atac matrix into a sparse Anndata:

Parameters

initial_matrix : initial dense count matrix to load and convert into a sparse matrix.

bed = True : If

should be the path to the bed file. : initial_matrix

output_file : name of the output file for the AnnData object.

output is the name of the input file with .h5ad extension : Default

path : path to the input count matrix. The AnnData object is written in the current directory,

not the location specified in path.

omic : 'ATAC', 'RNA' or 'methylation' are the 3 currently recognised omics in epiScanpy.

However, other omic name can be accepted but are not yet recognised in other functions. default: ‘ATAC’

bed : boolean. If True it consider another input format (bedtools output format for count matrices)

save : boolean. If True, the sparse matrix is saved as h5ad file. Otherwise it is simply return.

Returns

It returns the loaded matrix as an AnnData object.