Generalized fiducial methods for testing quantitative trait locus effects in genetic backcross studies

Abstract

In this paper, we propose generalized fiducial methods and construct four generalized p-values to test the existence of quantitative trait locus effects under phenotype distributions from a location-scale family. Compared with the likelihood ratio test based on simulation studies, our methods perform better at controlling type I errors while retaining comparable power in cases with small or moderate sample sizes. The four generalized fiducial methods support varied scenarios: two of them are more aggressive and powerful, whereas the other two appear more conservative and robust. A real data example involving mouse blood pressure is used to illustrate our proposed methods.

Keywords:

• Generalized fiducial inference
• quantitative trait locus
• mixture model
• Gibbs algorithm
• likelihood ratio test

Acknowledgments

We are grateful to the Associate Editor and two reviewers for their thorough reading of our manuscript and the constructive comments that lead to significant improvement of our work.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by the China Scholarship Council [Grant Number 201906140047] and National Natural Science Foundation of China [Grant Numbers 11801210, 11801359 and 11771145].