Issues about the ploidy_score cut-off

[SenLiBio]

Hi,

Thank you for developing CopyKit, and congratulations for publishing on Molecular Cell.

I have a question about the ploidy_score cutoff used after scquantum integer copy-number estimation. In the user guide and paper, I saw that cells with ploidy_score < 0.2 are kept.

Could you please clarify:

1. Why was 0.2 chosen as the threshold?
2. Is this value empirical, or does it have a theoretical interpretation from the confidence ratio / quantogram framework?
3. How would you recommend adjusting this cutoff for datasets with different coverage, noise levels, or ploidy complexity?

I am especially interested in how to choose an appropriate threshold for a new dataset rather than using 0.2 by default.

Thanks a lot.

Best,
Sen