MQM scan window size

[Nathaniel Burner]

Hi Karl,

I was wondering what the rationale is behind the default window size for mqmscan being 25. In CIM studies, I tend to see window sizes in the range of 2-10. For MQM, Jansen makes mention of using a window of 10-20 in the Quantitative Trait Loci in Inbred Lines chapter.

Thanks,

Nathaniel

[Karl Broman]

Personally I don't like the whole windowing business in CIM. I think those tall tight peaks with width equal to the window size are arbitrary and misleading.

The default window size in the cim() function is 10 cM and was chosen like 20 years ago.

I'm not sure of the origin of the default size of 25 cM in mqmscan(), but this was also a decision from at least 15 years past.

karl

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