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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