dynamo.pp.select_genes_monocle

dynamo.pp.select_genes_monocle(adata, layer='X', keep_filtered=True, n_top_genes=2000, sort_by='cv_dispersion', exprs_frac_for_gene_exclusion=1, genes_to_exclude=None, SVRs_kwargs={})[source]

Select genes based on monocle recipe.

This version is here for modularization of preprocessing, so that users may try combinations of different preprocessing procedures in Preprocessor.

Parameters:

  • adata (AnnData) – an AnnData object.

  • layer (str (default: 'X')) – The data from a particular layer (include X) used for feature selection. Defaults to “X”.

  • keep_filtered (bool (default: True)) – Whether to keep genes that don’t pass the filtering in the adata object. Defaults to True.

  • n_top_genes (int (default: 2000)) – the number of top genes based on scoring method (specified by sort_by) will be selected as feature genes. Defaults to 2000.

  • sort_by (Literal['gini', 'cv_dispersion', 'fano_dispersion'] (default: 'cv_dispersion')) – the sorting methods to be used to select genes. Should be one of the gini index or dispersion of coefficient variation or fano. Defaults to cv_dispersion.

  • exprs_frac_for_gene_exclusion (float (default: 1)) – threshold of fractions for high fraction genes. Defaults to 1.

  • genes_to_exclude (Optional[List[str]] (default: None)) – genes that are excluded from evaluation. Defaults to None.

  • SVRs_kwargs (dict (default: {})) – kwargs for SVRs. Defaults to {}.

Raises:

NotImplementedError – the ‘sort_by’ algorithm is invalid/unsupported.