snapatac2.pp.make_gene_matrix#

snapatac2.pp.make_gene_matrix(adata, gff_file, file=None, chunk_size=500, use_x=False, id_type='gene')[source]#

Generate cell by gene activity matrix.

Generate cell by gene activity matrix by counting the TN5 insertions in gene body regions. The result will be stored in a new file and a new AnnData object will be created.

Parameters

  • adata (AnnData | AnnDataSet) – The (annotated) data matrix of shape n_obs x n_vars. Rows correspond to cells and columns to regions.

  • gff_file (Genome | Path) – Either a Genome object or the path of a gene annotation file in GFF format.

  • file (Optional[Path]) – File name of the h5ad file used to store the result.

  • chunk_size (int) – Chunk size

  • use_x (bool) – If True, use the matrix stored in .X to compute the gene activity. Otherwise the .obsm['insertion'] is used.

  • id_type (Literal[‘gene’, ‘transcript’]) – “gene” or “transcript”.

Returns

A new AnnData object, where rows correspond to cells and columns to genes.

Return type

AnnData