HW 1 (10pts)
Define the following terms. You can use the definitions in the Sud et al review but use your own words. Provide a one-sentence summary definition and if you need more, write a longer multiple-sentence definition as well.
heritability
relative risk
Mendelian disease
cancer susceptibility genes
penetrance
risk allele frequency
odds ratios
linkage disequilibrium
effect size
pleiotropy
HW 1B (10 pts)
Run the logistic regression simulation code we discussed in class.
a). Annotate each step with an explanation of what it is doing.
b) Experiment with multiple values for the parameters, minor allele frequencies, and sample sizes. Comment on what you find.
c) The results (the output from R) with interpretation of what the estimates, standard errors, zscores, and p-values mean.
d) What’s the minimum sample size that yields a significant
HW 2 (10 pts)
Reproduce the simulations and code in https://bios25328.hakyimlab.org/post/2021/04/07/multiple-testing/
You are asked to turn in a
a) Knittable markdown document (5 points)
By knittable I mean that Anqi should simple load the Rmd in her Rstudio and click the knit button which should generate a nice HTML file viewable within Rstudio or with a web browser.
b) the Rmd should be annotated, explaining what is being done (5 points)
HW 2B (10 pts)
Following the scripts linked in https://bios25328.hakyimlab.org/post/2021/04/09/lab-2-gwas-in-practice/
Perform the GWAS and describe each of the figures generated
HW 3 (10 pts)
Run LD Score regression following steps here