𝕝ibrary(tidyverse) work.dir ="~/Downloads/hapmap/" ## qqunif function source("https://gist.githubusercontent.com/hakyim/38431b74c6c0bf90c12f/raw/21fbae9a48dc475f42fa60f0ef5509d071dea873/qqunif") Download plink for mac ## Download plink from https://www.cog-genomics.org/plink2 ## … Read more →

𝕝ibrary(tidyverse) ## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ── ## ✓ ggplot2 3.3.3 ✓ purrr 0.3.4 ## ✓ tibble 3.0.5 ✓ dplyr 1.0.3 ## ✓ tidyr 1.1.2 ✓ stringr 1.4.0 ## ✓ readr 1.4.0 ✓ forcats 0.5.0 ## ── Conflicts ────────────────────────────────────────── … Read more →

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𝕙ttps://uchicago.box.com/s/iqxg6yo7pi50hyudnfcv2xnhtfp6euv8 […] 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, let’s do the … Read more →

𝔾WAS: \(\boldsymbol{Y} = \boldsymbol{X}\beta + \boldsymbol{\epsilon}\) Example with n=4 \[\begin{bmatrix} y_1 \\ y_2 \\ y_3 \\ y_4 \end{bmatrix} = \begin{bmatrix} x_1 \\ x_2 \\ x_3 \\ x_4 \end{bmatrix}\cdot \beta + \begin{bmatrix} \epsilon_1 \\ \epsilon_2 \\ \epsilon_3 \\ \epsilon_4 \end{bmatrix}\] … Read more →

ℙroblem Set #1 Due on January 22nd by 1:50 pm Please email your pset answers to me (emcintire@uchicago.edu) with last week’s lab answers together as a single PDF. […] (10 points) Early onset Alzheimer’s disease is very rare; for illustrative purposes, assume it is 0.1% among adults aged … Read more →

𝕋hese papers can be good choices for the final presentations […] Sinnott-Armstrong, Nasa, FinnGen, Yosuke Tanigawa, David Amar, Nina Mars, Christian Benner, Matthew Aguirre, et al. 2021. “Genetics of 35 Blood and Urine Biomarkers in the UK Biobank.” Nature Genetics. … Read more →

𝕀n draft folder Gentle introduction to hypothesis testing from Kahn Academy A drug effect example of hypothesis testing and p-values from Kahn Academy Read more →

ℂreated by Max Winston, modified by Charles Washington III, Ankeeta Shah, Yanyu Liang, and Erik McIntire This lab section is dedicated to learning how to download HapMap data and manipulate the appropriate files in a command-line program named PLINK. Additionally, in R we will import data files and … Read more →

ℝ Markdown is a authoring framework that allows for reproducible documentation of data science within the context of R Studio. This is an introduction designed to teach you how to use R Markdown in a few minutes. Further info and some of the examples used below can be found here: … Read more →