W-test: dataset adaptive association test for main and interaction effects in GWAS data

 

  JC School of Public Health and Primary Care (JC SPHPC)  |  Faculty of Medicine |  The Chinese University of Hong Kong (CUHK)  |  Hong Kong SAR

 

 

 

Method

 

Download

 

Guide
      - R

      - C++

      - Linux

 

CCRB-Statgene

 

 

 Simulation study of main effect testing using W-test (k=2)

 

A. Simulation model of main effect: The genotype matrix is composed of 1,000 SNPs and 1,000 subjects. The phenotype is determined by setting Y equal to X1 or X2 at 20% probability, and Y has 60% probability of being a random 0 and 1. The genotype takes binary values under a dominant genetic model assumption.

 

   B. Results of simulation study:

 

Model

Methods

MAF > 5%

1%< MAF <5%

Power

(non-linear model)

Logistic

14.7%

62.8%

Chi-squared

81.0%

70.2%

W

87.1%

70.8%

Type I Error

Logistic

3.90E-05

4.00E-06

Chi-squared

0

0

W

7.00E-05

3.90E-05

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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