期刊
ANNALS OF HUMAN GENETICS
卷 73, 期 -, 页码 253-262出版社
WILEY
DOI: 10.1111/j.1469-1809.2008.00501.x
关键词
Nominal variables; Fisher's exact test; chi-square test; likelihood ratio test; Haldane test; measures of linkage disequilibrium
资金
- Biotechnology and Biological Sciences Research Council [BB/G000352/1] Funding Source: Medline
- Biotechnology and Biological Sciences Research Council [BB/G000352/1] Funding Source: researchfish
- BBSRC [BB/G000352/1] Funding Source: UKRI
This paper concerns several important points when testing for Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) in genetics. First, we challenge the necessity of using exclusively two-sided tests for LD. Next, we show that the exact 2-sided tests based on the most popular measures of LD are not equivalent, and neither are the standard statistical tests even though the 1-sided tests are equivalent. We show how this results in different inference about LD for two data sets consisting of small groups of markers. Finally, we advocate the use of the conditional p-value for both LD and HWE testing. An important advantage of this p-value is that equivalent 1-sided tests are transformed into equivalent 2-sided tests.
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