Question: discrepancy in the rehh results
2
gravatar for Ctanes
5.0 years ago by
Ctanes70
United States
Ctanes70 wrote:

Hello,

I am using the R package rehh to find SNPs that are undergoing positive selection in genomic regions of interest using the HapMap data. However I am having issues with the consistency of the results. If I have two overlapping regions: Chr1:151.8Mb-153.3Mb and Chr1:152.3-154.4Mb, the IHH, iES and iHS values are considerably different for the overlapping SNPs between the two regions. I would understand iHS being different since it is standardizing the results based on the SNPs that are in the same frequency bin. So the iHS values could potentially be different for a sliding region. But how are the IHH or the iES values different? Those calculations are based on the SNPs in a relatively close neighborhood of a central SNP, so the raw data is the same for the two regions. Did anyone else encounter this problem? Can anyone explain the reason for the discrepancies?

Thanks!

ADD COMMENTlink written 5.0 years ago by Ctanes70

Can you post a link to a paper describing iES... never heard of it?

ADD REPLYlink written 5.0 years ago by Zev.Kronenberg11k

Here is the link to the paper. http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0050171

It is the integrated Site Specific EHH and used for the pairwise population test (Rsb). I am not using Rsb yet for my research but I am more focused on the IHH (Integrated EHH) and the within population test (iHS).

ADD REPLYlink written 5.0 years ago by Ctanes70
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