omicverse.pp.filter_genes

omicverse.pp.filter_genes(adata, min_counts=None, min_cells=None, max_counts=None, max_cells=None, inplace=True)

Filter genes based on number of cells or counts.

Keep genes that have at least min_counts counts or are expressed in at least min_cells cells or have at most max_counts counts or are expressed in at most max_cells cells.

Only provide one of the optional parameters min_counts, min_cells, max_counts, max_cells per call.

Parameters:

• adata (AnnData) – An annotated data matrix of shape n_obs × n_vars. Rows correspond to cells and columns to genes.

• min_counts (Optional[int] (default: None)) – Minimum number of counts required for a gene to pass filtering.

• min_cells (Optional[int] (default: None)) – Minimum number of cells expressed required for a gene to pass filtering.

• max_counts (Optional[int] (default: None)) – Maximum number of counts required for a gene to pass filtering.

• max_cells (Optional[int] (default: None)) – Maximum number of cells expressed required for a gene to pass filtering.

• inplace (bool (default: True)) – Perform computation inplace or return result.

Returns:

• Depending on inplace, returns the following arrays or directly subsets

• and annotates the data matrix

• gene_subset – Boolean index mask that does filtering. True means that the gene is kept. False means the gene is removed.

• number_per_gene – Depending on what was tresholded (counts or cells), the array stores n_counts or n_cells per gene.