Should I use the "beta" estimates as the allelic effect size?

genetics-statistics / GEMMA

Genome-wide Efficient Mixed Model Association

https://github.com/genetics-statistics/GEMMA

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Should I use the "beta" estimates as the allelic effect size? #248

Open DuttaAnik opened 3 years ago

DuttaAnik commented 3 years ago

Hello, I have used gemma -lmm 2 for GWAS analyses. Now, the Reviewers want to see the allelic effect estimates of the significant SNPs. As I used the likelihood ratio test, it did not output the beta and se estimates. Now, I am re-analyzing the data with -lmm 1.

My question: is the beta estimates from the -lmm 1 can be reported as the allelic effect of the SNPs?

Please let me know.

Thank you.