【专题讨论】新年2010_gift:Hardy-Weinberg Equilibrium
在HWE检测中常用的是Pearson goodness-of-fit test,也就是我们常说的卡方检验因为近似于卡方分布。虽然这种方法容易计算,但是近似度不高特别是基因型数很低的时候,所以目前用Fisher exact test替代。
我给大家介绍一个目前公认source code!
分别用R,C/C++,Fortran写的!
若用此source code,写文章时候需引用如下:
A Note on Exact Tests of Hardy-Weinberg Equilibrium.
Wigginton JE, Cutler DJ and Abecasis GR
Am J Hum Genet (2005) 76: 887-93
Deviations from Hardy-Weinberg equilibrium (HWE) can indicate inbreeding, population stratification, and even problems in genotyping. In samples of affected individuals, these deviations can also provide evidence for association. Tests of HWE are commonly performed using a simple goodness-of-fit test. We show that this test can have inflated type I error rates, even in relatively large samples (e.g., samples of 1,000 individuals that include 100 copies of the minor allele). On the basis of previous work, we describe exact tests of HWE together with efficient computational methods for their implementation. Our methods adequately control type I error in large and small samples and are computationally efficient. They have been implemented in freely available code that will be useful for quality assessment o
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