A generalized Kruskal-Wallis test incorporating group uncertainty with application to genetic association studies

Biometrics. 2013 Jun;69(2):427-35. doi: 10.1111/biom.12006. Epub 2013 Feb 26.

Abstract

Motivated by genetic association studies of SNPs with genotype uncertainty, we propose a generalization of the Kruskal-Wallis test that incorporates group uncertainty when comparing k samples. The extended test statistic is based on probability-weighted rank-sums and follows an asymptotic chi-square distribution with k - 1 degrees of freedom under the null hypothesis. Simulation studies confirm the validity and robustness of the proposed test in finite samples. Application to a genome-wide association study of type 1 diabetic complications further demonstrates the utilities of this generalized Kruskal-Wallis test for studies with group uncertainty. The method has been implemented as an open-resource R program, GKW.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biometry / methods*
  • Chi-Square Distribution
  • Computer Simulation
  • Diabetes Mellitus, Type 1 / complications
  • Diabetes Mellitus, Type 1 / genetics
  • Genetic Association Studies / statistics & numerical data*
  • Genotype
  • Humans
  • Models, Statistical
  • Polymorphism, Single Nucleotide
  • Statistics, Nonparametric
  • Uncertainty