SPARC.__init__

Contents

SPARC.__init__#

missionbio.demultiplex.phylogeny.sparc.SPARC.__init__

SPARC.__init__(ado_score: float = 0.9, adjusted_mixing: float = 0.2, branch_size: int = 10, min_snv_clone_size: float = 0.001, min_snv_clone_count: int = 6, min_loh_clone_size: float = 0.001, min_loh_clone_count: int = 25, min_loh_group_size: int = 2, min_cnv_depth: int = 8, min_cnv_completeness: float = 0.6, min_copy_gain_cells: int = 150, min_excess_correlated_freq: float = 1) → None#
Parameters:

  • ado_score – Minimum ADO score to consider a clone valid.

  • adjusted_mixing – The maximum adjusted mixing rate to consider when looking for doublets.

  • branch_size – Controls the number of clones dropped in a given cycle. The run time is proportional to (branch_size ^ 3)

  • min_snv_clone_size – Minimum clone size as a fraction of the total for SNV clones to be considered. For rare variants, this limit might be ignored. It does not guarantee that all SNV clones will be larger than this value.

  • min_snv_clone_count – Minimum number of cells in a clone for the SNV clone to be considered. For rare variants, this limit might be ignored. It does not guarantee that all SNV clones will be larger than this value.

  • min_loh_clone_size – Minimum clone size as a fraction of the total for LoHFinder. It does not guarantee that all LoH clones will be larger than this value.

  • min_loh_clone_count – Minimum number of cells in a clone for LoHFinder. It does not guarantee that all LoH clones will be larger than this value.

  • min_loh_group_size – Minimum number of variants in a LoH variant group for it to be considered. Passed directly to LoHFinder.

  • min_cnv_depth – Minimum reads in each cell-amplicon for the completeness check

  • min_cnv_completeness – Minimum fraction of amplicons in a given cell with sufficient depth to be considered for amplicon modeling and copy gain prediction.

  • min_copy_gain_cells – The minimum number complete cells in a clone to consider it for copy gain clone identification

  • min_excess_correlated_freq – Minimum percentage of cells whose correlation is not due to random chance as per the chi2 expected frequencies. It is used to filter somatic variants that are not correlated with the CNV labels.

Contents