𝔻efine the following terms. You can use the definitions in the Sud et al review but use your own words. Provide a one-sentence summary definition and if you need more, write a longer multiple-sentence definition as well. heritability relative risk Mendelian disease cancer susceptibility genes … Read more →

𝕙ttps://www.icloud.com/keynote/0_qyvjHjowGtOqZd10GD470hA#L5-Population-Structure-PCA […] Mills, Melinda C.; Barban, Nicola; Tropf, Felix C.. An Introduction to Statistical Genetic Data Analysis (p. 237). MIT Press. Kindle Edition. […] J. Novembre, et al “Genes mirror geography within … Read more →

𝕎e will follow the tutorial published here by Marees et al A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis See the README file of the tutorial here […] If you want to work on the cluster you will need to load plink module avail ##Step 1 … Read more →

𝔽or a more detailed tutorial for GWAS analysis check out “A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis” by Mareen et al here. […] We will learn to run a GWAS using plink. This tutorial follows a plink tutorial you can find here […] … Read more →

𝕃et’s sample one value Z from the standard normal distribution set.seed(8050151) z1 = rnorm(1, mean=0, sd=1) z1 ## [1] -0.6089123 Let’s calculate now the p-value of this observation. Recall that the p-value is the probability that we will draw a sample as extreme as the observed value under the null … Read more →

𝕊ee the vignette here Read more →

𝕀n a population with random mating and no migration, most common variants will be at Hardy Weinberg Equilibrium (HWE). The genotype of a variant in HWE with minor allele (\(a\)) with frequency maf will be distributed as follows prob(AA): \(p = (1 - \text{maf})^2\) prob(Aa): \(2 \cdot \text{maf} … Read more →

ℂreated by Max Winston, modified by Charles Washington III, Ankeeta Shah, and Yanyu Liang (from HGEN47100 course material) Before getting started, please download data from the Box link here. For your convenience, we have a copy of the data folder at /project2/hgen47100/data/lab2 on midway. wget … Read more →

𝕙ttps://www.icloud.com/keynote/0dwLzjUpbNc3nVNxdrkvM-UHw#L3-Cancer-GWAS-QC (it takes a couple of minutes to set up the access the first time) […] Bycroft, C., Freeman, C., Petkova, D. et al. The UK Biobank resource with deep phenotyping and genomic data. Nature 562, 203–209 (2018). … Read more →

𝕃ogistic regression is the most common mode to model a binary outcome Y […] The log of the odds happens to be a very convenient quantity to be modeled as linear function of covariates: The log of the odds is modeled as a linear function of covariates \[Y \sim \text{Bernoulli}(\pi)\] \[ … Read more →