scmorph.pp.select_features

scmorph.pp.select_features#

scmorph.pp.select_features(adata, method='pearson', cor_cutoff=0.9, fraction=None, n_obs=None, copy=False)#

Feature selection

Select features by feature correlations. Allows measuring correlation on a subset of cells to speed up computations. See fraction and n_obs for details.

Parameters:

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

  • method (str (default: 'pearson')) – Which correlation coefficient to use for filtering. One of “pearson”, “spearman” and “chatterjee” ([[Lin and Han, 2021]]_)

  • cor_cutoff (float (default: 0.9)) – Cutoff beyond which features with a correlation coefficient higher than it are removed. Must be between 0 and 1.

  • fraction (float) – Subsample to this fraction of the number of observations.

  • n_obs (Optional[int] (default: None)) – Subsample to this number of observations.

  • copy (bool (default: False)) – Whether to return a copy or modify adata inplace (i.e. operate inplace)

Return type:

AnnData | None

Returns:

adata Feature correlations saved in .varm slot and feature selection saved in .var slot.

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