Genotypic variation

38 views
Skip to first unread message

seyma...@gmail.com

unread,
Mar 19, 2021, 1:46:13 PMMar 19
to R/qtl discussion
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

unread,
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.

karl

şeyma güneş

unread,
Mar 19, 2021, 1:58:19 PMMar 19
to rqtl...@googlegroups.com
Thank you Karl,
How about the calculation of R2 of the genotypic variation?



--
You received this message because you are subscribed to the Google Groups "R/qtl discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to rqtl-disc+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/rqtl-disc/fb44cbfc-5781-4b2c-ab5b-3b520713ec03n%40googlegroups.com.

Karl Broman

unread,
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.

karl
Reply all
Reply to author
Forward
0 new messages