Hello Everyone, I'm new to GWAS so forgive me for asking naive question. I have my summary statistics(From Linear mixed model) looks like below:
CHROM GENPOS ID ALLELE0 ALLELE1 A1FREQ INFO N TEST BETA SE CHISQ LOG10P
Allele0 is the reference allele and allele1 is the alternative allele. I wonder how to calculate R^2 from this summary. The GWAS model used normal approximation, 𝜒^2 chi-square to estimate the P-value.
I saw different equations such as
SNP (PVE) = [2*(beta^2)*MAF*(1-MAF)]/[2*(beta^2)*MAF(1-MAF)+((se(beta))^2)*2*N*MAF*(1-MAF)]
What's the best software to analyze the percentage of phenotypic variation explained by the identified SNPs?
Thank you very much!