infercnvpy.tl.cnv_score

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infercnvpy.tl.cnv_score#

infercnvpy.tl.cnv_score(adata, groupby='cnv_leiden', *, use_rep='cnv', key_added='cnv_score', inplace=True, obs_key=None)#

Assign each cnv cluster a CNV score.

Clusters with a high score are likely affected by copy number abberations. Based on this score, cells can be divided into tumor/normal cells.

Ths score is currently simply defined as the mean of the absolute values of the CNV scores in each cluster.

Parameters:

  • adata (AnnData) – annotated data matrix

  • groupby (str (default: 'cnv_leiden')) – Key under which the clustering is stored in adata.obs. Usually the result of infercnvpy.tl.leiden(), but could also be other grouping information, e.g. sample or patient information.

  • use_rep (str (default: 'cnv')) – Key under which the result of infercnvpy.tl.infercnv() is stored in adata.

  • key_added (str (default: 'cnv_score')) – Key under which the score will be stored in adata.obs.

  • inplace (bool (default: True)) – If True, store the result in adata, otherwise return it.

  • obs_key (default: None) – Deprecated alias for groupby.

Return type:

Mapping[Any, number] | None

Returns:

Depending on the value of inplace, either returns None or dictionary with the score per group.

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