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DReichLab / AdmixTools

Tools test whether admixture occurred and more
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how to explain the D-stastics result #26

Closed XuexueLiu closed 7 years ago

XuexueLiu commented 7 years ago

Dear @bumblenick in D-stastics README file, what's the meaning of "If the Z-score is +ve, then the gene flow occured either between W and Y or X and Z If the Z-score is -ve, then the gene flow occured either between W and Z or X and Y." and I got the result : W X Y Z 0.0027(Dstat) 1.496337525(Z score) 335725(BABA) 7196699(ABBA), so W and Y or X and Z had gene flow? thankyou

bumblenick commented 7 years ago

Please tell me the version # of qpDstat. It looks like you have run into a formatting bug with the BABA count merging with Z. If your version is current I'll fix quickly, But this is a Z score of 1.496, not significant with flow W <-> Y or X <-> Z

Nick

On Mon, Jun 12, 2017 at 11:04 AM, XuexueLiu notifications@github.com wrote:

Dear @bumblenick https://github.com/bumblenick in D-stastics README file, what's the meaning of "If the Z-score is +ve, then the gene flow occured either between W and Y or X and Z If the Z-score is -ve, then the gene flow occured either between W and Z or X and Y." and I got the result : W X Y Z 0.0027(Dstat) 1.496337525(Z score) 335725(BABA) 7196699(ABBA), so W and Y or X and Z had gene flow? thankyou

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/DReichLab/AdmixTools/issues/26, or mute the thread https://github.com/notifications/unsubscribe-auth/AQn_hwMyhMO0WmABjmNw0lqn05In26-zks5sDVN_gaJpZM4N3Pxh .

bumblenick commented 7 years ago

There was a formatting issue in qpDstat, now I hope fixed.

Nick

On Mon, Jun 12, 2017 at 11:29 AM, Nick Patterson nickp@broadinstitute.org wrote:

Please tell me the version # of qpDstat. It looks like you have run into a formatting bug with the BABA count merging with Z. If your version is current I'll fix quickly, But this is a Z score of 1.496, not significant with flow W <-> Y or X <-> Z

Nick

On Mon, Jun 12, 2017 at 11:04 AM, XuexueLiu notifications@github.com wrote:

Dear @bumblenick https://github.com/bumblenick in D-stastics README file, what's the meaning of "If the Z-score is +ve, then the gene flow occured either between W and Y or X and Z If the Z-score is -ve, then the gene flow occured either between W and Z or X and Y." and I got the result : W X Y Z 0.0027(Dstat) 1.496337525(Z score) 335725(BABA) 7196699(ABBA), so W and Y or X and Z had gene flow? thankyou

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/DReichLab/AdmixTools/issues/26, or mute the thread https://github.com/notifications/unsubscribe-auth/AQn_hwMyhMO0WmABjmNw0lqn05In26-zks5sDVN_gaJpZM4N3Pxh .

XuexueLiu commented 7 years ago

Dear Nick I used the ## qpDstat version: 662 thankyou!

bumblenick commented 7 years ago

Latest version should fix the formatting problem. You are likely using a dataset with a very large # of SNPs. You should consider thinning it.

N

On Tue, Jun 13, 2017 at 11:08 AM, XuexueLiu notifications@github.com wrote:

Dear Nick I used the ## qpDstat version: 662 thankyou!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/DReichLab/AdmixTools/issues/26#issuecomment-308147868, or mute the thread https://github.com/notifications/unsubscribe-auth/AQn_h9u6TqLKIYE_4bHsVVAnX1Lq9USTks5sDqYGgaJpZM4N3Pxh .