Question: Function returning % trait explained for a SNP given effect size, MAF, prevalence, etc. for a complex trait
1
gravatar for Vincent Laufer
13 months ago by
Vincent Laufer1.1k
United States
Vincent Laufer1.1k wrote:

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: https://s15.postimg.cc/ev42ffx6z/var_exp_stahl_2012.png

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:

heritability - https://cran.r-project.org/web/packages/heritability/heritability.pdf

genabel - http://forum.genabel.org/viewtopic.php?f=6&t=134#p202

rrBLUP - https://www.nature.com/articles/s41437-017-0023-4

will update further once I can evaluate each package.

ADD COMMENTlink modified 13 months ago by zx87547.9k • written 13 months ago by Vincent Laufer1.1k

Not an R package, but maybe: http://cnsgenomics.com/software/gcta/#Overview

ADD REPLYlink written 13 months ago by zx87547.9k
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