Week 6 Feedback

[dtaylo95]

README.md with commands and analyses

2/2

Exercise	Points Possible	Grade
Commands for Step 1.1	0.33	0.33
Commands for Step 2.1	0.33	0.33
Commands for Step 3.1	0.33	0.33
Answer to Step 3.4	1	1

I'm not sure what happened with your answer to 3.4, but I'm getting a different gene than you. I have the same top hit as you (rs10876043), but when I look it up, it's in the DIP2B gene. I wonder if you might have been using the wrong version of the reference (we're on hg18). No points off, just wanted to point that out.

plotting.py script to produce plots

3.75/4

Exercise	Points Possible	Grade
Code to produce step 1.2 PC plot	1	1
Code to produce step 2.2 AFS plot	1	1
Code to produce step 3.2 Manhattan plots	1	0.75
Code to produce step 3.3 effect size boxplot	1	1

Very minor issue, but it looks like you're plotting ALL of your associations in your manhattan plots, rather than just the genotype associations. To clarify: when you run your GWAS, you include the top PCs as covariates in the regression (this is correct). But this means that you also get regression results for the covariates, not just the variants you're testing. Take a look at the TEST column in the .assoc.linear output file(s) of the plink --linear command to figure out which results you want to keep/plot.

Pretty plots

4/4

Exercise	Points Possible	Grade
Step 1.2 PC plot	1	1
Step 2.2 AFS plot	1	1
Step 3.2 Manhattan plots	1	1
Step 3.3 effect size boxplot	1	1

Grade

Total: 9.75/10

Great work! Feel free to fix that one minor issue and resubmit for full credit!

[Joseph-Dixon1]

I've uploaded it now

[Joseph-Dixon1]

uploaded readme.md

[dtaylo95]

Great work! I regraded it and updated the rubric above. Again, feel free to fix that one small thing and resubmit