XPEHH output

[paolo002]

Hi I have obtained an output of the XPEHH but there are only two columns. One, for the SNP IDs and the second the XPEHH values. First of all, is this normal? Because in the manual it is indicated that 5 columns will be present in the output. If yes, may I know if the values should be considered as hap popA compared to hap popB or vice versa? Thanks

[camaclean]

I double checked the source files. It should be:

Location    iHH_A1    iHH_B1    iHH_P1    XPEHH

XPEHH = log(A1/B1)

This reminds me that I need to finish implementing standardizing the xpehh values. Right now, you have to do that manually.

[paolo002]

Thank you very much. I understand. I think the output of the iHS is giving me two files, one with values before normalisation and the other with values after it (*.std) while the XPEHH is giving only one file. In both cases the files have only two columns. Then, how to normalise the XPEEH values? And, if XPEHH=log(A1/B1), does it mean that a positive value equals to selection on population A while negative value equals to selection on population B? Am I correct? By the way, congratulations for developing hapbin, I compared it with selscan using the same input dataset and the iHS results are as good as selscan but it saved me a lot of time because selscan is extremely slow while hapbin can give the results thousands time faster for both iHS ands XPEHH.

[paolo002]

hi, please, can you let me know how to normalise the XPEEH scores? Does it need the info of the HH_A1 and iHH_B1?, because it is not in the output.

[prenderj]

Hi

Yes if have a high (standardised) XP-EHH value then suggests that EHH decays more slowly in population A suggesting its haplotypes have potentially been under stronger positive selection.

The normalisation procedure is the same as for iHS i.e. for each XP-EHH value you determine how many standard deviations from the mean of other values it is (https://en.wikipedia.org/wiki/Standard_score). Hopefully Colin can implement this.

Best Wishes James

On Mon, 17 Sep 2018 at 09:41, paolo002 notifications@github.com wrote:

hi, please, can you let me know how to normalise the XPEEH scores?

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[paolo002]

Thanks a lot for the explanation.

[camaclean]

I just realized I'd already implemented it, but forgot to push the addition. Pull #47 does it.

[paolo002]

Thank you very much! Really appreciated.

[camaclean]

Wait for pull #48 before using the non-MPI version. I have a bug in #47 when calculating frequency.

[paolo002]

Sure, thanks a lot Colin

[paolo002]

Hi , I am sorry, I forgot to ask also some explanation about the iHS instead. For the Hapbin iHS output, a positive standardised value of iHS equals to selection on the reference allele while a negative value is equal to selection on alternate allele? Is that correct?