Function returning % trait explained for a SNP given effect size, MAF, prevalence, etc. for a complex trait
0
1
Entering edit mode
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: 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.

risk score genetic variance explained R • 838 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1572 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6