Approximations to Est and Est.SE in GENESIS
1
0
Entering edit mode
@stephanie-m-gogarten-5121
Last seen 13 hours ago
University of Washington

Question submitted via email:

I am using GENESIS R package to fit GLMM models to analyze genome-wide associations of SNPs with binary traits in a dataset with familial design. Running the "fitNullModel" and "assocTestSingle" functions (with family = "binomial" and test="Score") the results return Score/Score.SE for each SNP and, in addition, contain Est/Est.SE which are (according to user manual) approximations of effect sizes and their standard errors.

I appreciate if you can clarify if these Est/Est.SE approximations are based on a Wald's test? and if the family is kept as binomial or internally changed to gaussian to decrease the computational burden when Est/Est.SE are computed?

Also, is my understanding correct that when a GXE term is included, the effect sizes (Est.G, Est.G:env) are based on a Wald’s test and a binomial family?

GENESIS • 802 views
ADD COMMENT
0
Entering edit mode
@stephanie-m-gogarten-5121
Last seen 13 hours ago
University of Washington

Est is not recalculated, rather it is approximated based on the score test results, as described in this paper. Est = Score/(Score.SE^2) and Est.SE = 1/Score.SE. When a GxE term is included, the effect sizes are similarly approximated based on a multi-parameter score test.

ADD COMMENT

Login before adding your answer.

Traffic: 853 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