3) Problem Set

Problem Set

All required data files are located in the New_Gwas_Workshop folder. We will be using the problem_set_phenotype.txt file for this problem set.

1. Is the problem set phenotype normally distributed? Did you need to adjust the phenotype prior to running your analysis?

2. Show the plink command you used to run your GWAS below and explain what each option within the command does.

3. I'm not good with numbers. Can you visually show me the significant SNPs? Make a Q-Q plot and a Manhattan plot of the results. Attach the plots into this document and write a figure legend similar to scientific papers explaining what each plot means.

4. What does the Q-Q plot indicate about the data? Are there potential confounders in the data that indicate further analysis is required?

5. Based on the Manhattan Plot, are there any genome-wide significant hits? What test allows you to see this and also correct for multiple hypothesis testing? Explain why.

6. Let's move to LocusZoom. Looking at your top SNPs, is there any functional information known about them? If they're located on or near a gene, which one? How may these loci be functioning in response to Lu Wolf's spirit? Include screenshots from Locuszoom or other appropriate databases in your answer.

7. Make a plot and legend of your top hit's genotype vs phenotype. Is the minor allele associated with an increase or decrease in spirit?

8. An important aspect of research is knowing what to do with your findings. What analyses or experiments could be done to follow up on your findings?