𝕊torey & Tibshirani, “Statistical significance for genomewide studies,” Proceedings of the National Academy of Sciences, Jul. 2003. […] UK Biobank Imputed Genotype Data Release Bycroft, C., Freeman, C., Petkova, D., Band, G., Elliott, L. T., Sharp, K., et al. (2018). The UK Biobank … Read more →

ℝeview of concepts in probabiliy and statistics […] Review probability […] Maximum Likelihood Estimation […] Bayesian Inference […] Probability cheatsheet: this cheatsheet will be handy throughout the course for your reference. It’s a highly condensed summary of this … Read more →

𝕎e want to calculate the power to detect an association a genetic marker and a quantitative phenotype. […] As a concrete example, we pre-specify the model for continuous trait \(Y\) and genotype \(X\) as \[Y = \beta X + \epsilon, ~~~~ \text{with } \epsilon \sim N(0, \sigma_\epsilon^2)\] where … Read more →

𝕀n this exercise, you will use LD score regression method to calculate the partitioned heritability of GWAS phenotype from UK Biobank. Below is a step by step guide on setting up and running the analysis. […] If you have conda installed on your machine skip this step Installation […] … Read more →

𝔽ind the slides here Read more →

𝔽ind slides here Read more →

𝕋he genetic relatedness matrix (which can be used to calculate heritability and also to adjust for relatedness and population structure) encodes the structure of the data. To get an intuitive sense of how that works, do the following. […] (10 points) Calculate GRM of hapmap_chr22 data … Read more →

𝔽ind the class notes here […] Example of mixed effects model to account for population structure […] Relating Z-scores, p-values, and chi2 Read more →

ℕotice that the estimated effect size divided by the standard error behaves like a normal(0,1) random variable when the sample size is large enough: […] \[ Z = \frac{\hat\beta}{\text{se}(\hat\beta)}\] \[Z \approx N(0,1) ~~~~~~ \text{as } n \rightarrow \infty\] Let’s simulate zscore vector … Read more →

𝕋otal of 40 points Download hapmap3 data in plink format from https://uchicago.box.com/s/84de60jj4j9nyhl7nc7lylk4fcq12eka […] Hint: you can borrow code with the appropriate modifications from https://hgen471.hakyimlab.org/post/2021/02/18/l6-population-structure/ Read more →