Ctrl+K

scgenome.pp.calculate_filter_metrics

scgenome.pp.calculate_filter_metrics#

scgenome.pp.calculate_filter_metrics(adata, quality_score_threshold=0.75, read_count_threshold=500000, copy_state_diff_threshold=1.0, inplace=False)#

Calculate additional filtering metrics to be used by other filtering methods.

Parameters:

  • adata (AnnData) – copy number data on which to calculate filter metrics

  • quality_score_threshold (float, optional) – The minimum quality to set to keep, by default 0.75

  • read_count_threshold (int, optional) – The minimum total mapped reads from hmmcopy to set for keeping, by default 500000

  • copy_state_diff_threshold ([type], optional) – Minimum copy-state difference threshold to set to keep, by default 1.

  • inplace (bool, optional) – Whether to modify passed in AnnData, by default False

Returns:

AnnData with modified obs if not inplace, otherise, None

Return type:

AnnData

Note

The following properties are changed: - AnnData.obs.filter_quality - AnnData.obs.filter_reads - AnnData.obs.filter_copy_state_diff

If is_s_phase is a property of AnnData

AnnData.obs.filter_is_s_phase

AnnData.obs.copy_state_diff AnnData.obs.copy_state_diff_mean