Exact Tests for Hardy-Weinberg Proportions
Exact Tests for Hardy-Weinberg Proportions
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DOI：
10.1534/genetics.109.108977
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发表时间：
2009-12-01
期刊：
影响因子：
3.3
通讯作者：
Engels, William R.
中科院分区：
文献类型：
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作者：
Engels, William R.
精确的条件检验通常需要在统计学上评估二倍体样本是否符合Hardy-Weinberg比例或确认基因型分配的准确性。当样本包括多个等位基因和稀疏数据时，这种要求尤其常见，从而使渐近方法（如常见卡方检验）不可靠。这种精确检验可以使用似然比作为其检验统计量来执行，而不是更常用的概率检验。讨论了似然比的概念优势。一个大大改进的算法，允许性能的一个完整的枚举精确测试的样本量太大，以前的方法。本文还提出了一种改进的蒙特卡罗算法。排除完全枚举。这些算法比目前使用的算法快两个数量级。最后，方法推导出一个给定的集合来计算可能的样本的数量。的等位基因计数，一个有用的数量，用于评估的可行性，充分计数程序。提供了实现这些方法的软件ExactoHW。
Exact conditional tests are often required to evaluate statistically whether a sample of diploids comes front a population with Hardy-Weinberg proportions or to confirm the accuracy of genotype assignments. This requirement is especially common when the sample includes multiple alleles and sparse data, thus rendering asymptotic methods, such as the common chi(2)-test, unreliable. Such an exact test can be performed using the likelihood ratio as its test statistic rather than the more commonly used probability test. Conceptual advantages ill using the likelihood ratio are discussed. A substantially improved algorithm is described to permit the performance of a full-enumeration exact test on sample sizes that are too large for previous methods. An improved Monte Carlo algorithm is also proposed for samples that. preclude full enumeration. These algorithms are about two orders of magnitude faster than those currently ill use. Finally, methods are derived to compute the number of possible samples with a given set. of allele counts, a useful quantity for evaluating the feasibility of the full enumeration procedure. Software implementing these methods, ExactoHW, is provided.