search

jiabowang / GAPIT

Genome Association Predict Integrate Tools
171 stars 55 forks source link

How do I prepare phenotype data for analyzing binary traits? #107

Open jeong2624 opened 9 months ago

jeong2624 commented 9 months ago

Hello!

I'm planning to use GAPIT for GWAS data analysis. However, my phenotype data is categorical, while the models provided by GAPIT are based on numerical data.

The GAPIT manual mentions that GAPIT can analyze binary traits (case-control), but it doesn't explain how explicitly.

If I want to analyze binary traits using GAPIT, should I encode them as 0 and 1 in the phenotype data?

Also, if the phenotype data consists of nominal or categorical values, could you please explain how to analyze it with GAPIT?

Lastly, can you confirm if all GAPIT models are available for this scenario?

jiabowang commented 7 months ago

Yes, the GAPIT works for binary traits and continuous traits. But in the binary traits, the heritability is always low. So the detectability of GWAS always shows no-enough. That needs many more individuals.