I am conducting GWAS using GAPIT R package with FarmCPU model. However, unlike GLM and MLM, GAPIT does not produce R2 when FarmCPU model is used. I tried to work around this by using the linear model function in R (lm) like this: fit
Ahmed Warsame
I found the solution in this paper.
https://www.frontiersin.org/articles/10.3389/fgene.2019.00302/full
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Peymaneh Davoodi
Hi
Also, you can get more help here from these two powerful papers:
https://www.nature.com/articles/nature09270
http://www.nature.com/ncomms/journal/v2/n9/full/ncomms1467.html
Best regards
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Ahmed Warsame
Hi Peymaneh Davoodi thanks for the suggestion. I am going to read these papers too.
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