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UW-GAC / GENESIS

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
https://bioconductor.org/packages/GENESIS
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Estimate PVE #96

Closed MARCPUCV closed 1 year ago

MARCPUCV commented 2 years ago

Hi, I would like to know how the PVE is calculated. I have the data from the GMMAT package and I don't know how to estimate the PVE of the significant snps. I saw that with your package it can be calculated but I have had problems with the installation of the GENESIS and GWASTools packages. Thank you very much.

Best regards!! Angélica

mconomos commented 2 years ago

Hello, In GENESIS, the individual variant PVE is approximated from the score test statistic and the residual sum of squares for the null model. Specifically, the approximated PVE = (Score.Stat)^2/RSS0, where Score.Stat = score/SE(score) and RSS0 is the residual sum of squares from the null model.

For details of the explanation/derivation, please see the section "Proportion of Variance Explained Jointly by a set of variants" from the supplemental materials of this manuscript: https://pubmed.ncbi.nlm.nih.gov/33887194/