Week 6 Feedback

[dtaylo95]

README.md with commands and analyses

1.67/2

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
Answer to Step 3.4	1	1

Still missing your commands for step 3.1 (running the linear regression with plink)

plotting.py script to produce plots

2.75/4

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	0

Still missing the boxplot.

Also, for your manhattan plot, 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

3/4

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	0

Still missing the boxplot

Grade

Total: 7.42/10

[jadecathy]

Hi Dylan,

I uploaded the week6 homework. Sorry I accidentally also uploaded the eigenvalue file and cannot pull it back from the repository. Thank you in advance!

[dtaylo95]

Hey! I've updated the feedback/rubric above. Nice work, but still missing the boxplot and there were some minor issues with the manhattan plot. Feel free to address those and submit another re-grade