Multiple LOD peaks per chromosome

[Ted Monyak]

Hi,

I am trying to figure out if there is functionality in r/qtl to extract multiple LOD peaks per chromosome. It seems like most of the functions (such as lodint(), summary()) only return the max LOD peak per chromosome. I am interested in doing this with the output of a scanone() object, as well as with the output of a scantwo() object.

Thanks!

[Karl Broman]

R/qtl1 doesn’t have any code to pick out multiple peaks on a chromosome in scanone output. For scantwo, you can look at evidence for a second QTL, given the first on a chromosome. 

Rather than try to identify the multiple peaks in the output of scanone, I would encourage you to fit multiple-QTL models, such as with fitqtl().

karl

[Ted Monyak]

Got it, thanks for the suggestion. It looks like the find_peaks() function in R/qtl2 might have the functionality of what I'm looking for?