I got a position that does not exist

[Madi Shoken]

Hi Karl, 

I got one position in find_peaks() results that is not in the gene map at all, but QTL analysis shows this result as if this position is in my gene map. Why does it show this? Can you tell me what the problem is?

Regards

Madi

[Karl Broman]

I can’t say anything without more details.

karl

[Karl Broman]

In the find_peaks function, if the maximum LOD score is hit at multiple positions, the position reported will be the average of those positions.

As a result, the reported peak position may not be at a marker position.

In the Details section of the help file, it says:

> At a given peak, if there are ties, with multiple positions jointly achieving the maximum LOD score, we take the average of these positions as the location of the peak.

Also note that with "riself" data, genotypes need to be coded as AA = 1 and BB = 2. (AB genotypes get ignored.)

In the control file, use geno_codes = list(AA=1, BB=2)

If you were to use geno_codes=list(AA=1, AB=2, BB=3), you'd end up ignoring the BB genotypes and treating the AB genotypes as if they were BB.

karl