Homework 5

1 Download data from

https://uchicago.box.com/s/iqxg6yo7pi50hyudnfcv2xnhtfp6euv8

2 Q1 Visualize Family Structure in Genetic Relatedness Matrix

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 following. (Hint: check code here https://github.com/hakyimlab/hgen471/blob/master/analysis/L8-GRM.Rmd)

1. Calculate GRM of hapmap_chr22 data

2. Select a couple of CEU families and a couple of YRI families. Plot (tile plot)

3. What structure do you see? Do you see family structure?

3 Q2 Plot the $\chi^2$ statistic vs. LD score

To get an intuitive sense of how LD-score regression works, check the code https://github.com/hakyimlab/hgen471/blob/master/analysis/L8-LD-score.Rmd and complete the followings.

1. Plot the histogram of LD-score

2. Plot $\chi^2$ statistic vs. LD-score

3. Regress $\chi^2$ on LD-score