Open sandyplus opened 3 years ago
Hi Sandy,
Sorry for the long delay in responding! I've been trying to double check things to see where the discrepancy between the paper and the code arises and it's mainly in how things are ordered when the test is done.
The short answer is that you are correct that the gamma reported by HyDe is the proportion of the genome from P1.
I'll keep you posted of any changes but please also let me know if there is anything else
Dear @pblischak , In your paper "HyDe: A python package for genome-scale Hybridization detection", it suggests that the gamma is the probabilities of P2.
However, in your source code, it suggested that gamma is the probabilities of P1:
Moreover, our results suggested that the gamma in out-filtered.txt should be the probabilities of P1 (I calculated gamma in out-filtered.txt manually, and found that the gamma = 1 - (AABB-ABAB)/(AABB+ABBA-2*ABAB)).
I am confused about the "gamma" in filtered-out.txt. Would you mind give me any suggestion?
Best regards, Sandy
PS: the test results: