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

plotting.py script to produce plots

3.5/4

Exercise	Points Possible	Grade
Code to produce step 1.2 PC plot	1	0
Code to produce step 2.2 AFS plot	1	0
Code to produce step 3.2 Manhattan plots	1	0.75
Code to produce step 3.3 effect size boxplot	1	0.75

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.

ALSO. I'm not sure if it's because you're including the covariates in the analysis but the top hit you're getting for the GS451 (rs17113501) is not the top hit I'm getting (rs7257475). That said, I tried running your code (covariates included) and I still get rs7257475 as the top hit, so I'm not sure what's going on on your end. If you do re-make the plot with the rs7257475 variant, make sure you include all three genotypes!

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: 9.5/10

Great work! Just a couple very minor issues that you're welcome to address and resubmit

[dtaylo95]

Graded! Feel free to address the two minor comments and resubmit for 10/10