GEMMA GWAS how to specify factor or numerical for covariates

Question

[mawigoj318]

Dear all,

I am doing gwas analyses using GEMMA and want to use both location and a continuous variable as covariates. I have 5 locations coded as 1,2,3,4,5 and the continuous variable range from 1-70.

I followed the gemma manual when creating the covariate file, including an intercept as the first column. My issue is that it does not appear anywhere in the manual how do specify that my location should not be treated as a continuous variable but as a factor. I am wondering anyone had a similar concern and if they found a solution?

[Sofia]

Hi, I don't have a solution to your question but I followed this tutorial and was helpful to me in my analysis https://youtu.be/NusV6duyvXs