confused results of gamma

[sandyplus]

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:

cpdef dict test_triple(self, str p1, str hyb, str p2):
        """
        Main method for testing a hypothesis on a specified triple.
        ((P1,Hyb),P2)::math:`\gamma` and (P1,(Hyb,P2))::math:`1-\gamma`.
        ...
        """

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:

P1	P1	Hybrid	P2	Zscore	Pvalue	Gamma	AAAA	AAAB	AABA	AABB	AABC	ABAA	ABAB	ABAC	ABBA	BAAA	ABBC	CABC	BACA	BCAA	ABCD
sp1	sp1	i6	sp3	1.593522109	0.055521558	0.074873654	895827	47673	45106	31853	4386	63858	15012	4055	16375	101188	5967	4019	5371	8899	411
sp1	sp1	i7	sp3	2.60956678	0.004532883	0.114143664	895408	48097	45525	31774	4041	63297	14669	3779	16873	101249	6128	4082	5653	9102	323
sp1	sp1	i8	sp3	2.962820534	0.00152424	0.122324308	893470	47230	47463	32558	4124	63085	14599	3916	17102	101899	5959	4065	5073	9103	354
sp1	sp1	i9	sp3	2.307708986	0.010507637	0.103607183	894791	48019	46142	31712	4181	63504	14789	3997	16745	101024	5926	4003	5758	9049	360
sp1	sp1	i10	sp3	1.771350954	0.038251133	0.080454255	894980	47790	45953	32129	3993	63940	14882	3933	16391	101904	6330	3921	4785	8772	297

[pblischak]

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