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PankratzLab / GenScorePipeline

Genetic Score Pipeline, Merge Extract Pipeline
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Add calculation for percent variance explained #5

Open kbeutel opened 1 year ago

kbeutel commented 1 year ago

GSP needs to calculate the percent variance explained via a simple formula

npankrat commented 1 year ago

PVE: estimated proportion of total variance explained using the formula from Shim et al. 2015 (https://doi.org/10.1371/journal.pone.0120758.s001)

All this needs is beta, SE, and sample size (N) to compute. Technically allele frequency is part of the computation as well, but since it's in the numerator and the denominator, the value doesn't affect the end result. Here is an example within Excel:

beta SE MAF N estRsq -10.637 2.07 0.083534137 3735 0.007020167

Where the formula for estRsq is =2*POWER(A2,2)*C2*(1-C2)/(2*POWER(A2,2)*C2*(1-C2)+POWER(B2,2)*2*D2*C2*(1-C2))