omicverse.pp.filter_cells

omicverse.pp.filter_cells(adata, min_counts=None, min_genes=None, max_counts=None, max_genes=None, inplace=True)[source]

Filter cell outliers based on counts and numbers of genes expressed.

For instance, only keep cells with at least min_counts counts or min_genes genes expressed. This is to filter measurement outliers, i.e. “unreliable” observations.

Only provide one of the optional parameters min_counts, min_genes, max_counts, max_genes per call.

Parameters:

  • adata (AnnData) – The (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 cell to pass filtering.

  • min_genes (Optional[int] (default: None)) – Minimum number of genes expressed required for a cell to pass filtering.

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

  • max_genes (Optional[int] (default: None)) – Maximum number of genes expressed required for a cell 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

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

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