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evotools / hapbin

Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)
GNU General Public License v3.0
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xpehh p value calculation #62

Open devenderarora opened 4 years ago

devenderarora commented 4 years ago

Dear Sir, I have performed xpehhbin and found xpehh value from the repective program. I am interested in P-Value is there any way to calculate the same?

prenderj commented 4 years ago

Hi

XP-EHH scores are analogous to standard scores ( https://en.wikipedia.org/wiki/Standard_score) in that they represent how many standard deviations from the mean of all values in a particular frequency bin a given value is. For this reason previous studies have used a cutoff of 2 as a Z of 2 roughly equates to a p value of 0.05. However this doesn't account for multiple testing and is therefore a lenient threshold. Other approaches are probably better, for example permuting population labels, recalculating XP-EHH and observing how often values as extreme as those in the real data are observed.

Cheers James

On Mon, 8 Jun 2020 at 08:27, devenderarora notifications@github.com wrote:

Dear Sir, I have performed xpehhbin and found xpehh value from the repective program. I am interested in P-Value is there any way to calculate the same?

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devenderarora commented 4 years ago

Thankyou sir for giving the direction.