Is there a version of permuteGPAT that can permute XP-EHH score ?

[xiagjt]

Hi. It is so good for me to use your code like GPAT. Recently, I am calculating the XP-EHH for a crop population. I have got the XP-EHH scores for every SNP site, However, I have no idea to do the permutation for a p value. Could you tell me how to do that ? Thanks in advance!

[zeeev]

@xiagjt If you're taking the absolute value of XP-EHH (abs(XP-EHH)) you can just match the wcFst format and use the permuteGPAT++ code.

[xiagjt]

The XP-EHH is directional. If I want to keep the negative value, the permuteGPAT++ code will work ? OR I follow your suggestion and append the P value to the previous directional XP-EHH score.

[krystal915]

hi, zeeev! permuteGPAT++ is really a exellent tool! You said that we can match the wcFst format and use the permuteGPAT++ code to test other dataset. I wonder if the 'format' you mean is just the column number and oder, which do not related with its content.
eg. "scaffold1 0 20000 512 0.157" is the same as "scaffold1 1 1 1 0.157" when appling permutation test!

cheers!

[zeeev]

Hi @krystal915,

Thanks for the kind words. You're absolutely correct, just match the column number and order. I would also recommend that you use the main VCFLIB (https://github.com/vcflib/vcflib). It has the same functionality, but I'm not supporting this fork anymore.

--Zev