<p>I have calculated XP-EHH and iHS scores for a set of snps using selscan. XP-EHH ranges from -0.75 to 0.9. What do extreme values show? In the original<a href="http://www.nature.com/nature/journal/v449/n7164/full/nature06250.html"> publication</a> they plot log(P-value). I think that P-values was calculated to show differences between xp-ehh and iHS. Does anyone have experience with selection scores?</p>

<p>XP-EHH is a cross-population test for positive selective. It means that it detect SNPs that are under selection in one population but not in another. For example a SNP associated to resistance to malaria may be under selection in populations where malaria has been endemic but under neutral selection in other populations. It was developed because it is generally very difficult to identify signals of selection in a population, and comparing two populations may allow to identify weaker signals that are evident only after comparing with a closely related population.</p>

<p>The sign of the XP-EHH score indicates which of the two alleles is under selection, e.g. whether the ancestral or the derived allele. For practical reasons, people usually tend to ignore the sign and use the absolute XP-EHH score. This is because you may not always be sure about which SNP is ancestral in which population. Moreover taking the absolute score makes it easier to calculate mean by sliding windows.</p>

<p>In the publication they used -log(p-value), probably as a way to simplify the interpretation of the data in the plot. The value is usually generated by sorting the scores and taking the rank of them - e.g. see how I answered Zev in this discussion: https://www.biostars.org/p/94421/#163632 . The p-value is then converted to -log(p-value) to facilitate the interpretation. For example a p-value of 0.01 becomes -log(0.01) = 2, so you can say that all SNPs with a -log(p-value) higher than 2 are significantly selected in one population.</p>
