Testing Hardy-Weinberg equilibrium with a simple root-mean-square statistic

Biostatistics

Volumn 15, Issue 1, 2014, Pages 74-86

  Ward, Rachel ^a   Carroll, Raymond J ^b  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

Absolute discrepancies; Hardy Weinberg equilibrium; Relative discrepancies; Root mean square

Indexed keywords

ABSOLUTE DISCREPANCIES; ALGORITHM; ALLELE; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENOTYPE; HARDY-WEINBERG EQUILIBRIUM; HUMAN; MONTE CARLO METHOD; RELATIVE DISCREPANCIES; ROOT MEAN SQUARE;

ABSOLUTE DISCREPANCIES; HARDY-WEINBERG EQUILIBRIUM; RELATIVE DISCREPANCIES; ROOT MEAN SQUARE;

ALGORITHMS; ALLELES; COMPUTER SIMULATION; GENOTYPE; HUMANS; MODELS, GENETIC; MONTE CARLO METHOD;

EID: 84890471620     PISSN: 14654644     EISSN: 14684357     Source Type: Journal    
DOI: 10.1093/biostatistics/kxt028     Document Type: Article

References (31)

1. AYRES, K. AND BALDING, D. (1998). Measuring departures from Hardy-Weinberg: a Markov chain Monce Carlo method for estimating the inbreeding coefficient. Heredity 80, 769-777. (Pubitemid 28329395)
2. BICKEL, P., RITOV, Y. AND STOKER, T. (2006). Tailor-made tests for goodness of fit to semiparametric hypotheses. Annals of Statistics 34, 721-741. (Pubitemid 44091390)
3. BROWNLEE, K. (1965). Statistical Series and Methodology in Science and Engineering. New York: Wiley.
4. CHEN, J. AND THOMSON, G. (1999). The variance for the disequilibrium coefficient in the individual Hardy-Weinberg test. Biometrics 55, 1269-1272.
5. CONSONNI, G., MORENO, E. AND VENTURINI, S. (2011). Testing Hardy-Weinberg equilibrium: an objective Bayesian analysis. Statistics in Medicine 30, 62-74.
6. COUNCIL, NATIONAL RESEARCH. (1996). The Evaluation of Forensic DNA Evidence. Washington, DC: National Academy Press.
7. DIACONIS, P. AND STURMFELS, B. (1998). Algebraic algorithms for sampling from conditional distributions. Annals of Statistics 26(1), 363-397.
8. EFRON, B. AND TIBSHIRANI, R. (1993). An Introduction to the Bootstrap. Boca Raton, FL: Chapman and Hall.
9. ENGELS, W. (2009). Exact tests for Hardy-Weinberg proportions. Genetics 183(4), 1431-1441.
10. GELMAN, A. (2003). A Bayesian formulation of exploratory data analysis and goodness-of-fit testing. International Statistical Review 71, 369-382. (Pubitemid 37052986)
11. GIBBONS, J. AND PRATT, J. (1975). P-values: interpretation and methodology. The American Statistician 29(1), 20-25.
12. GUO, S. AND THOMPSON, E. (1992). Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48, 361-372.
13. HARDY, G. (1908). Mendelian proportions in a mixed population. Science 28, 49-50.
14. HENZE, N. (1996). Empirical-distribution-function goodness-of-fit tests for discrete models. The Canadian Journal of Statistics 24(1), 81-93. (Pubitemid 126312176)
15. LAURETTO, M., NAKANO, F., FARIA, S., PEREIRA, C. AND STERN, J. (2009). A straightforward multiallelic significance test for the Hardy-Weinberg equilibrium law. Genetics and Molecular Biology 32(3), 619-625.
16. LI, Y. AND GRAUBARD, B. (2009). Testing Hardy-Weinberg equilibrium and homogeneity of Hardy-Weinberg disequilibrium using complex survey data. Biometrics 65, 1096-1104.
17. LINDLEY, D. (1964). The Bayesian analysis of contingency tables. The Annals of Mathematical Statistics 35(4), 1622-1643.
18. MAISTE, P. AND WEIR, B. (1995). A comparison of tests for independence in the FBI RFLP data bases. Genetica 96(1-2), 125-138.
19. PERKINS, W., TYGERT, M. AND WARD, R. (2011). Computing the confidence levels for a root-mean-square test of goodness of fit. Applied Mathematics and Computation 217, 9072-9084.
20. PERKINS, W., TYGERT, M. AND WARD, R. (2012). Computing the confidence levels for a root-mean-square test of goodness of fit, II, in preparation.
21. PERKINS, W., TYGERT, M. AND WARD, R. (2013). Some deficiencies of chi-square and classical exact tests of significance. Applied and Computational Harmonic Analysis, to appear.
22. 2 test of goodness of fit. Journal of the American Statistical Association 70(352), 811-813.
23. RAYMOND, M. AND ROUSSET, F. (1995). An exact test for population differentiation. Evolution 49(6), 1280-1283. (Pubitemid 3025486)
24. RORI, R. AND WEIR, B. (2008). Distributions of Hardy-Weinberg equilibrium test statistics. Genetics 180(3), 1609-1616.
25. SHAM, P. (2001). Statistics in Human Genetics. London: Arnold Publishers.
26. SHOEMAKER, J., PAINTER, I. AND WEIR, B. (1998). A Bayesian characterization of Hardy-Weinberg disequilibrium. Genetics 149, 2079-2088. (Pubitemid 28375973)
27. TYGERT, M. (2012). Testing the significance of assuming homogeneity in contingency-tables/cross-tabulations, in preparation.
28. WAKEFIELD, J. (2010). Bayesian methods for examining Hardy-Weinberg equilibrium. Biometrics 66(1), 257-265.
29. WEINBERG, W. (1908). Über den nachweis der vererbung beim menschen. Jh. Ver. vaterl. Naturk. Wurttemb. 64, 369-382. (English translations in BOYER 1963 and JAMESON 1977).
30. WEISING, K. (2005). DNA Fingerprinting in Plants: Principles, Methods, and Applications. Boca Raton, Florida: Taylor and Francis.
31. WIGGINTON, J., CUTLER, D. AND ABECASIS, G. (2005). A note on exact tests of Hardy-Weinberg equilibrium. American Journal of Human Genetics 76(5), 887-893. (Pubitemid 40563110)