Genotypic variation

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Mar 19, 2021, 1:46:13 PMMar 19
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Hi Karl,

I have an F2 population and I conducted single interval mapping with transform data, I would like to know the units of the additive and dominance effects (% of variation or trait unit).  Also, I would like to calculate heritability and include R2 of the genotypic variation. 
Do you have any suggestions?



Karl Broman

Mar 19, 2021, 1:51:43 PMMar 19
to R/qtl discussion
Estimated additive and dominance effects can be obtained from fitqtl() with the argument get.ests=TRUE. They're simply regression coefficients with a particular encoding for the genotypes. Or you can think of them as differences between phenotype averages. If you provide a transformed phenotype, the estimated coefficients will be on that transformed scale.

You can get the estimated percent variance explained by QTL from fitqtl() with the argument dropone=TRUE.


şeyma güneş

Mar 19, 2021, 1:58:19 PMMar 19
Thank you Karl,
How about the calculation of R2 of the genotypic variation?

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Karl Broman

Mar 19, 2021, 2:19:34 PMMar 19
to R/qtl discussion
I'm not sure what that means, other than just being another term for heritability.

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