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NVIDIA-Genomics-Research / GEPSi

GEPSi simulates phenotypes for GWAS data based on a range of conditions and biological assumptions.
Apache License 2.0
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Heritability added incorrectly #13

Open RossDeVito opened 6 days ago

RossDeVito commented 6 days ago

In the paper and implementation you add noise to the genetic component of the phenotype to reach a desired heritability using:

g' = h * g + sqrt(1-h^2) N(0, 1), where h = heritability

There may have been confusion due to heritability typically being written as h^2, but the correct equation should be:

g' = sqrt(h^2) * g + sqrt(1-h^2) N(0, 1), where h^2 = heritability

or

g' = sqrt(h) * g + sqrt(1-h) N(0, 1), where h = heritability

RossDeVito commented 6 days ago

I have a branch that fixes this, but it doesn't seem like I have permission to push

RossDeVito commented 6 days ago

Here is the fix: https://github.com/NVIDIA-Genomics-Research/GEPSi/commit/13315fa84db854daaf455fd824eb5e3e477ddfe3

RossDeVito commented 6 days ago

14