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xiaolei-lab / rMVP

:postbox: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study
Apache License 2.0
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use significant SNP as CV, permutation of FarmCPU #14

Closed tanyongjun0815 closed 6 years ago

tanyongjun0815 commented 6 years ago

Hi Xiaolei, thank you for develop such a convenient package. I have some questions: 1, I hve read your paper on plos genetics, I think FarmCPU can detect epstasis loci. But new loci ware detected when previous significant SNP added to CV (somebody call this SNP-fix, p value of new loci was just excess the threshold). is that needed to add significant SNP as CV for FarmCPU model? 2, when I use permutation to set threshold on farmcpu model, MVP display "GLM", is that right? can you tell me? (my statistics backgroud was weak, you just need tell me what was right) thank you.

hyacz commented 6 years ago

Q1:
You don't have to manually add SNP as CV, FarmCPU will do this, automatically.

Q2:
May be a display error. When you set maxLoop to 1, the FarmCPU is equivalent to GLM, but he should still display “FarmCPU”.

tanyongjun0815 commented 6 years ago

OK, i got it, thanks for your reply.

hyacz commented 6 years ago

closed. if you have any other questions, feel free to open a new issue.