Question: Gwas Quantitative Trait Power Calculation
2
gravatar for Joey
7.2 years ago by
Joey20
Joey20 wrote:

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

Thanks,

gwas • 12k views
ADD COMMENTlink written 7.2 years ago by Joey20
4
gravatar for Neilfws
7.2 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 7.2 years ago by Neilfws48k
4
gravatar for Larry_Parnell
7.2 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink written 7.2 years ago by Larry_Parnell16k
3
gravatar for Aaronquinlan
7.2 years ago by
Aaronquinlan10k
United States
Aaronquinlan10k wrote:

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

ADD COMMENTlink written 7.2 years ago by Aaronquinlan10k

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?

ADD REPLYlink written 7.2 years ago by Joey20
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