Entering edit mode
8.9 years ago
Tohamy ▴ 80
I have a simple question. How can I calculate genetic correlation between two traits (at different environments) with R?
I calculated the phenotypic correlation and heritability for the interested traits but now I need to calculate genetic correlation between the traits.
Which function is used for that in R?
To provide a good answer to this question we'd to know what your data looks like and what you mean by genetic correlation (which sounds pretty similar to heritablity, which you've already calculated?)
(Whoops, I'd skipped over the fact you have two measured traits, and genetic correlation is therefore the shared genetic contribution to the two traits. It's possible to fit multi-response models with R, but readers probably still need to know a bit more about your data to provide an answer)
META-R can generate for you both phenotypic and genetic correlations among all the traits. It is a free click click version of r developed by CYMMIT. https://data.cimmyt.org/dataset.xhtml?persistentId=hdl:11529/10201
Meta-R does it nicely. Nice suggestion
Several years ago I published a paper in which I analysed heritability of several quantitative traits, and I remember that I used the software package SOLAR by John Blangero's group to calculate genetic correlation. Maybe you can give a look in the methods used by SOLAR and see if you can figure it out. I never tried calculating heritability or genetic correlation using R, so in this respect I cannot help...
You might want to compare the rankings of significant SNPs in two traits, again as DavidW mentioned, we need to know more about data.