How to calculate genetic correlation with R
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8.6 years ago
Tohamy ▴ 80

Hey all,

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?

Best Regards,

Tohamy

R • 8.9k views
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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?)

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(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)

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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

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Meta-R does it nicely. Nice suggestion

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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...

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You might want to compare the rankings of significant SNPs in two traits, again as DavidW mentioned, we need to know more about data.

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