Hi Everyone,

I am anew in this. So forgive me if anything asking stupid! I calculated genome-wide standardized iHS and XP-EHH scores from 'Selscan' software. They both are present in negative and positive values. i read in some papers people choose |iHS| > 2 as a significant region cut-off, but i have read no cutoff for XP-EHH.

For XP-EHH values, i calculated p-values using 'pnorm' in R something like:

```
data<-read.table("CHR.xpehh-norm.reformat1.txt",header=FALSE,sep=" ")
p<-vector()
for (i in 1:dim(data)[1])
{if (data[i,4]>0)
p[i]<-pnorm(data[i,4],lower.tail=FALSE)
else p[i]<-pnorm(data[i,4],lower.tail=TRUE)
}
write.table(p,file="xpehh.p.chr.txt")
```

I have later read about p-values/Zscore calculation at C: A Database Of Signatures Of Selection In The 1000 Genomes Dataset

Problems:

can anyone please guide me how to correctly calculate the p-values for XP-EHHH and iHS scores (am i doing right in above mentioned scenario??).

and in iHS case we are considering only absolute values, how to calculate p-values for that?

and is there any general cutoff standardized scores (like |iHS| > 2) for the scores calculated by these two tests, so that selective outliers can be identified?

Thanks a lot in advance!

Hi, I am facing the same problem as you had with calculating the p-value from XP-EHH scores. Just wondering if you figured it out? If possible, could you please share the final solution? Much appreciated.