How to calculate OR/Beta for each gene using SKAT.SSD.All

[shaolei teng]

Hi

I'm using SKAT.SSD.All to perform burden analysis of gene/genesets for case-control and quantitative trait data. I used three approaches SKAT, BURDEN (r.corr=1), SKATO (method="optimal.adj") in the function. The outputs just gave the P-value and No of all/test markers for each gene. How to calculate the odds ratio / beta for each gene using SKAT (maybe only for BURDEN?)? Thus, I can know whether the variants excess in cases or controls. Thanks!

Shaolei

[Seunggeun (Shawn) Lee]

Hi Shaolei,

SKAT doesn't provide an odds ratio/ beta estimate of each gene, since it is designed to test for association, not estimating the effects. You only can estimate odds ratio/beta under the Burden test framework. SKAT package doesn't provide any function for it, but I think you can do it very easily using a genotype matrix, which can be obtained using Get_Genotypes_SSD.

Thanks,

Shawn 

[Kousik Kundu]

Hello,
Is there any example of how to calculate the beta for the burden test from metaSKAT output, please?
For the above reply (though quite old), it seems the beta/effect can be caluclated using p-value and the genotype matrix?

[Xiaochen Liu]

Just checking..does anyone figure out how to calculate beta using genotype matrix?

[jing wang]

 I also want to know how to calculate the effect size.