smftools.tools.cluster_adata_on_methylation

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smftools.tools.cluster_adata_on_methylation#

smftools.tools.cluster_adata_on_methylation(adata, obs_columns, method='hierarchical', n_clusters=3, layer=None, site_types=('GpC_site', 'CpG_site'))#

Add clustering groups to adata.obs based on methylation patterns.

Parameters:

adata (AnnData) -- AnnData object to annotate.
obs_columns (Sequence[str]) -- Observation columns to define subgroups.
method (str (default: 'hierarchical')) -- Clustering method ("hierarchical" or "kmeans").
n_clusters (int (default: 3)) -- Number of clusters for k-means.
layer (str | None (default: None)) -- Layer to use for clustering.
site_types (Sequence[str] (default: ('GpC_site', 'CpG_site'))) -- Site types to analyze.

Return type: