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
) – The data from a particular layer (include X) used for feature selection. Defaults to “X”.keep_filtered (
bool
) – Whether to keep genes that don’t pass the filtering in the adata object. Defaults to True.n_top_genes (
int
) – 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'
]) – 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
) – threshold of fractions for high fraction genes. Defaults to 1.genes_to_exclude (
Optional
[List
[str
]]) – genes that are excluded from evaluation. Defaults to None.SVRs_kwargs (
dict
) – kwargs for SVRs. Defaults to {}.
- Raises:
NotImplementedError – the ‘sort_by’ algorithm is invalid/unsupported.