Function returning % trait explained for a SNP given effect size, MAF, prevalence, etc. for a complex trait
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2.7 years ago
Vincent Laufer ★ 1.1k

Hello all,

Is there a function written in R or another language of the form:

Variance_Explained <- get_var_exp(effect_size, minor_allele_frequency, [other args])


Specifically, on page 25 of the supplemental methods of Stahl et al. 2012 (see https://www.nature.com/articles/ng.2232 ), an equation for variance explained is given:

It returns the percent variance of a trait that a given variant accounts for, given effect size (in either beta or odds ratio) and MAF. Coding this would not be particularly difficult, but there are a couple assumptions made that add some leg work (need liability threshold assumptions and I have other necessary parameters such as population prevalence (1%)). Is anyone aware of a function that is already written that will do this?

Update: I have located a few packages that tackle similar problems:

will update further once I can evaluate each package.

risk score genetic variance explained R • 838 views
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Not an R package, but maybe: http://cnsgenomics.com/software/gcta/#Overview