This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Gwas Quantitative Trait Power Calculation

What do you use for power calculation for a GWAS with a quantitative trait?

Thanks,

gwas
• 17,076 views • link
updated by Larry_Parnell Larry_Parnell • written by Joey • Joey

3 answers

Have not tried them, but some options are:

  • GWAPower: a statistical power calculation software for genome-wide association studies with quantitative traits
  • GWASpower/QT: a statistical power calculation software designed for genome wide association studies (GWAS) with quantitative traits in natural populations
  • The GenABEL suite

Unsure on which platform the first two run (possible Windows only); GenABEL is popular with the R user community (cross-platform).

See also the CRAN task view for more R-based genetics packages.

• 201 views • link
updated by Ram Ram • written by Neilfws Neilfws

We use Quanto for traits like triglyceride levels in blood and body mass index, assuming no family relationship (very important not to overlook!) and an additive model. We also use Quanto when considering gene-environment interactions in the power calculation.

• 109 views • link
written by Larry_Parnell Larry_Parnell

Have a look at this post on Getting Genetics Done. PS Power ostensibly handles continuous traits.

• 2 views • link
written by Aaronquinlan Aaronquinlan

so.. the minor allele frequency doesn't play a role in power calculation for a quantitative phenotype...I got a beta coefficient value of 0.28 for the top snp and the snp had a maf of 0.35. Is there any place I can add that? Also, it says that the maximum # of levels is 12 for the trait. What does it exactly mean?

• 0 views • link
written by Joey • Joey

Log in to answer this question.

More posts like this