hibayes PVE or GVE of snp marker

Hello,

When using variable selection method on markers, how do you calculate variance explained both genetic and phenotypic of all snps? I tried to follow the example in vignette but I am getting a lower sum PEV explained of all markers than snp heritability

Dec 11 '23 19:12 statslover123

Thank you for the question. In hibayes package, the heritability of a trait is derived from dividing the genetic variance by the sum of genetic variance, residual variance, and all the environmental variance, rather than dividing the variance of original phenotype. And the PVE in GWAS study, we usually pay more attention to the contribution of a marker to the original phenotype, thus we divide it by the variance of original phenotype here. It should be noted that the sum of PVE is not comparable with the SNP heritability, because the markers are not fully independent from each other, they are in linkage disequilibrium.

Dec 12 '23 02:12 YinLiLin

Thank you, how can we calculate genetic variance explained per a snp?

Dec 27 '23 06:12 statslover123