elizeng
commented
4 months ago Managed to get all permutations I wanted by specifying a tree: (((N1,N2,N3,N4),(S1,S2,S3,S4,S5,S6,S7,S8)),Outgroup)
Closed elizeng closed 4 months ago
elizeng
commented
4 months ago Managed to get all permutations I wanted by specifying a tree: (((N1,N2,N3,N4),(S1,S2,S3,S4,S5,S6,S7,S8)),Outgroup)
I have specific permutations that I am interested in testing for introgression.
Context: I have 12 populations: N1-4, S1-8
I am interested in testing for introgression for the specific permutations where P1 and P2 comprise of N1-4, and P3 of S1-8.
Using Dtrios, I get scenarios where the S population is assigned to P1 and while N populations are in P2 and P3, for which the statistical values cannot be easily converted. Example: Permutation I get with Dtrios: P1 P2 P3 S1 N1 N2
Permutation that I am interested in P1 P2 P3 N2 N1 S1
The ouput from Dtrios for the former permutation: Dstatistic Z-score p-value f4-ratio BBAA ABBA BABA 0.033719 16.5261 2.30E-16 0.141038 102944 101308 94698.7
Given that D stats is minimized for each trio, would other combinations then be significant for introgression?
I have also tried using the tree function, but it seems that I would require a tree comprising all populations rather than making a simple tree for P1, P2, P3, O. I do not have a tree for all populations at the moment.
Would appreciate any suggestion for whether it is possible to set up the analysis for specific permutations.
Cheers!