Homework 3

Assignment

1. Download HapMap3 chromosome 22 data (5pt)
2. Download Growth Data (5pt)
3. Calculate PCs using plink (10pt)
4. Plot the first two principal components of the genotype matrix, color by population (10pt)
5. Run GWAS of growth with and without adjusting for PCs (20pt)
   1. show qqplot and manhattan plot for each (10pt)
6. Create HapMap Trios Relatedness Matrix (10pt)
7. generate a tileplot to visualize the population and relatedness patterns here (10pt)

See below for additional information on the assignment.

Links

• You can borrow code from here
  • https://hakyimlab.github.io/hgen471/L6-population-structure.html
  • https://bios25328.hakyimlab.org/post/2020/02/06/l8-grm/
• slides

  • Lecture 5 https://docs.google.com/presentation/d/1VYfx0coU5HKQLXwbo5yr7XvgJeqt8Hdf/edit#slide=id.p1

  • Lecture 6

    https://docs.google.com/presentation/d/1I0-4u_6PAG5Q9LNi3mfQNnvZsVgf16tO/edit#slide=id.p1

Introduction

The main goal of this of this homework is to reproduce and interpret the graphs that were shown in this week’s lectures. This document will walk you through getting the data and installing plink in order to run through the code.

Submit the report as a a knitted document of your choice( ex: pdf, html, etc.).

Note: be sure that the code is visible in the final document knitted document.

Downloading the Data and Plink

For this homework you will need to two data folders and install and set up plink. You can use your local device for this. If you have trouble installing plink, you can use the Rstudio cloud.

Download the hapmap3 genotype files in plink format (bed/bim/fam), here we are linking to the subset of chromosome 22 to keep files small.

wget https://uchicago.box.com/s/uu5fbx135qgp37spnrrsxrk4acuibkwh
wget https://uchicago.box.com/s/eh0thcbeo5sb1ywufrowtm3uqqgad0b2
wget https://uchicago.box.com/s/7py9smo190ucl6jrdwe0de8wjdc6rrwq

• You can find the full HapMap 3 genotype data with other useful information here https://uchicago.app.box.com/folder/155475906095?s=84de60jj4j9nyhl7nc7lylk4fcq12eka
• Growth phenotype Data
  • https://github.com/hakyimlab/igrowth/blob/master/rawgrowth.txt
  • if you want background information on this trait you can read https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002525)

Plink

You will need to use Plink for this homework. Please refer back to the lab posted here if you have questions on commands and syntax. You will want to set the path as described in step 1 of the Lab as well.

Downloading Plink

wget https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20220305.zip
##Use this link if you are on Rstudio Cloud otherwise go to the website
##https://zzz.bwh.harvard.edu/plink/download.shtml 
unzip plink_linux_x86_64_20220305.zip
mikdir bin 
mv plink bin