def filter_genes_cv_deprecated(X, Ecutoff, cvFilter):
"""Filter genes by coefficient of variance and mean.
See `filter_genes_dispersion`.
Reference: Weinreb et al. (2017).
"""
if issparse(X):
raise ValueError('Not defined for sparse input. See `filter_genes_dispersion`.')
mean_filter = np.mean(X, axis=0) > Ecutoff
var_filter = np.std(X, axis=0) / (np.mean(X, axis=0) + .0001) > cvFilter
gene_subset = np.nonzero(np.all([mean_filter, var_filter], axis=0))[0]
return gene_subset
def zscore_deprecated(X):
"""Z-score standardize each variable/gene in X.
Use `scale` instead.
Reference: Weinreb et al. (2017).
Parameters
----------
X : np.ndarray
Data matrix. Rows correspond to cells and columns to genes.
Returns
-------
XZ : np.ndarray
Z-score standardized version of the data matrix.
"""
means = np.tile(np.mean(X, axis=0)[None, :], (X.shape[0], 1))
stds = np.tile(np.std(X, axis=0)[None, :], (X.shape[0], 1))
return (X - means) / (stds + .0001)