Genotypic variation

[seyma...@gmail.com]

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?

Thanks,

Seyma

[Karl Broman]

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.

karl

[şeyma güneş]

Thank you Karl,

How about the calculation of R2 of the genotypic variation?

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[Karl Broman]

I'm not sure what that means, other than just being another term for heritability.

karl