Question

Gwas Quantitative Trait Power Calculation

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12.2 years ago

Joey ▴ 20

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

Thanks,

gwas • 16k views

ADD COMMENT • link updated 12.2 years ago by Larry_Parnell 16k • written 12.2 years ago by Joey ▴ 20

Ram · Answer 1 · 2012-01-23

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.

score 4 · Answer 2 · 2012-01-23

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12.2 years ago

Larry_Parnell 16k

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 COMMENT • link 12.2 years ago by Larry_Parnell 16k

score 3 · Answer 3 · 2012-01-23

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12.2 years ago

Aaronquinlan 12k

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

ADD COMMENT • link 12.2 years ago by Aaronquinlan 12k

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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 REPLY • link 12.2 years ago by Joey ▴ 20