Homework 5

Haky Im

2021-02-12

Categories: homework

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?

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

Reuse

Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The source code is licensed under MIT.

Suggest changes

If you find any mistakes (including typos) or want to suggest changes, please feel free to edit the source file of this page on Github and create a pull request.

Citation

For attribution, please cite this work as

Haky Im (2021). Homework 5. BIOS 25328 Cancer Genomics Class Notes. /post/2021/02/12/homework-5/

BibTeX citation

@misc{
  title = "Homework 5",
  author = "Haky Im",
  year = "2021",
  journal = "BIOS 25328 Cancer Genomics Class Notes",
  note = "/post/2021/02/12/homework-5/"
}