Multiple LOD peaks per chromosome

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Ted Monyak

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1:13 PM (2 hours ago) 1:13 PM

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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

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1:32 PM (2 hours ago) 1:32 PM

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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().