# scvelo.pp.filter_genes_dispersion¶

scvelo.pp.filter_genes_dispersion(data, flavor='seurat', min_disp=None, max_disp=None, min_mean=None, max_mean=None, n_bins=20, n_top_genes=None, retain_genes=None, log=True, subset=True, copy=False)

Extract highly variable genes.

Expects non-logarithmized data. The normalized dispersion is obtained by scaling with the mean and standard deviation of the dispersions for genes falling into a given bin for mean expression of genes. This means that for each bin of mean expression, highly variable genes are selected.

Parameters: data : AnnData, np.ndarray, sp.sparse The (annotated) data matrix of shape n_obs × n_vars. Rows correspond to cells and columns to genes. flavor : {'seurat', 'cell_ranger', 'svr'}, optional (default: 'seurat') Choose the flavor for computing normalized dispersion. If choosing ‘seurat’, this expects non-logarithmized data - the logarithm of mean and dispersion is taken internally when log is at its default value True. For ‘cell_ranger’, this is usually called for logarithmized data - in this case you should set log to False. In their default workflows, Seurat passes the cutoffs whereas Cell Ranger passes n_top_genes. max_mean=3, min_disp=0.5, max_disp=None : min_mean=0.0125, If n_top_genes unequals None, these cutoffs for the means and the normalized dispersions are ignored. n_bins : int (default: 20) Number of bins for binning the mean gene expression. Normalization is done with respect to each bin. If just a single gene falls into a bin, the normalized dispersion is artificially set to 1. You’ll be informed about this if you set settings.verbosity = 4. n_top_genes : int or None (default: None) Number of highly-variable genes to keep. retain_genes : list, optional (default: None) List of gene names to be retained independent of thresholds. log : bool, optional (default: True) Use the logarithm of the mean to variance ratio. subset : bool, optional (default: True) Keep highly-variable genes only (if True) else write a bool array for highly-variable genes while keeping all genes. copy : bool, optional (default: False) If an AnnData is passed, determines whether a copy is returned. If an AnnData adata is passed, returns or updates adata depending on copy. It filters the adata and adds the annotations