Lecture 3, Oct 3, 2025 Slides Jupyter Notebook The dataset I used in the Lecture can be downloaded here . HW 3 (Due Oct 10, Friday). 1 . A SNP locus is genotyped for a total of 1000 individuals, among which 485 is AA, 421 is Aa, and 94 is aa. Compute the $X^2$ statistic for Hardy-Weinberg Equilibrium, and find the P-val. You can either use function pchisq or use your simulated reference distribution. 2. Genetic Association Test Genetic Association studies have been very popular in last two decades. Billions of dollars have been spent and tens of millions individuals have their genomes genotyped. They all look for a simple signal. That is, the distribution of genotypes differ among people with different phenotypes. Consider a study with diabetes. Say we recruited 1000 diabetes patients, and 1500 controls. Assume that they are from the same genetic background, which is very important. If the patients are recruited in US, and co...
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