estimating gen maps

[Fernando Andrade]

Hello Karl, how are you doing?

I was trying to use QTL2 to get loci position in cM for an F69 AIL but I got some huge gaps in my map (like going from ~6cM to 108cM and even more in other positions). Jim Cheverud told me that they were using qtl (insteald of qtl2) to estimate the map positions back in the F44. Is there any significant difference between est_map() (qtl2) and est.map() (qtl)?

Also, is there any way to convert the qtl2 cross to qtl, so I can use the "older" functions?

Thanks

Fernando

[Karl Broman]

There’s little difference betwen est.map() in R/qtl1 and est_map() in R/qtl2, other than that in R/qtl1 it is implemented only for backcross, intercross, and RIL, while in R/qtl2 it can be applied, in principle, to more cross types, including in principle ail. But I think it’s not actually been implemented for ail; you’re presumably treating the cross as an f2? The results should be identical between R/qtl1 and R/qtl2 for an f2.

Unfortunately, I don’t have a way to convert cross objects from R/qtl2 back to the R/qtl1 format.

karl

[Fernando Andrade]

Yep, I am treating them as F2s.

Do you have any recommendation to check for these huge gaps that est_map() is creating? Do you think the functions on qtl would be a  better way to study these problems? I saw here (https://rqtl.org/tutorials/geneticmaps.pdf) that qtl has many features to try to understand problems that may come with the map, but I do not know any of these function in qtl2.

Thanks for your prompt response

Fernando

[Karl Broman]

Yes, the functions in r/qtl1 would be useful. But the basic diagnostics are not particularly complicated. The main things I would look at would be the genotype frequency at the individual markers, and then the 2-way tables of genotype frequencies for pairs of adjacent markers. The error LOD scores may also be useful.

karl

On Apr 14, 2025, at 2:03 PM, Fernando Andrade <fernand...@gmail.com> wrote:



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[Fernando Andrade]

thanks!