Logistic regression for GWAS analysis

Hi, I would like to know how a logistic regression in a GWAS works in detail.

I have an example dataset, with SampleIDs, Genotypes (GT) in dosage formt and binary phenotypes. Now, how would the logistic regression be performed if I only want to work with the allele counts/frequencies and not the genotypes? Or is the logistic regression always performed on the genotypes? Does PLINK also calculate it on the genotypes?

Does it make sense to calculate a 2×3/2×2 contingency table first?

```
SNP1
SampleID GT Pheno
Sample1 1 1
Sample2 0 0
Sample3 2 0
Sample4 0 1
Sample5 1 1
```

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