homework 4 - polygenic risk scores

A. Complete the following assessments

• Lecture 6 assessment quiz (10 points)
• Lecture 7 assessment quiz (10 points)

B. Finish the knit lab 4 (70 points)

In this section, you will complete the practical implementation of polygenic risk scoring using PRSice software as done in Lab 04. As a reminder, it involves:

1. Setting up the environment and downloading necessary data:
   • Download and install PRSice software
   • Set up the Personal Genome Project data
   • Install required R packages (tidyverse, RSQLite, glue)
2. Data exploration and preparation:
   • Explore the phenotype database
   • Analyze demographic distributions
   • Create phenotype data files for analysis
3. Running PRSice analysis:
   • Compute polygenic risk scores for height
   • Use UK Biobank height GWAS results as the base data
   • Apply various p-value thresholds for score calculation
4. Results analysis and visualization:
   • Plot observed versus predicted height values
   • Perform regression analysis to assess prediction accuracy
   • Interpret the results in the context of polygenic prediction

The lab will help you understand: - The practical implementation of PRS calculations - The relationship between GWAS results and phenotype prediction - The challenges and limitations of polygenic risk scoring - The interpretation of PRS results in real-world data

Make sure to document your code, results, and interpretations clearly in your knitted document. The grading will focus on: - Correct implementation of the analysis pipeline - Quality of data visualization - Clarity of interpretation - Proper documentation of the process

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