Week 6 Feedback

[dtaylo95]

README.md with commands and analyses

0/2

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

3.75/4

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

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 didn't take off points for this), but in your boxplot, typically we organize the x-axis as heterozygous samples being in between the two different homozygotes. 1) we often expect the phenotype of heterozygotes to be intermediate between the two homozygous genotypes. Obviously this isn't always the case, such as for mendelian dominant/recessive traits, but it's often a good rule of thumb. 2) When we run our linear regression in the GWAS, what we're actually doing is fitting a line to the points formed when you organize the x-axis this way. The slope of the line is then "how much does the trait change when you add one additional alternative allele.

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 address the minor issue(s) and resubmit for full credit!

[lws99]

I have done most of week 6!

[dtaylo95]

Hi Logan! Thanks for uploading! I've updated the rubric above. Please feel free to resubmit again if you want to fix that one small error. It should hopefully be very quick/easy