search

tttan14 / qbb2023-answers

0 stars 0 forks source link

Week 6 Feedback #5

Open dtaylo95 opened 10 months ago

dtaylo95 commented 10 months ago

README.md with commands and analyses

/2

Exercise Points Possible Grade
Commands for Step 1.1 0.33 0
Commands for Step 2.1 0.33 0
Commands for Step 3.1 0.33 0
Answer to Step 3.4 1 0

Your README.md uploaded, but it looks like it's blank

plotting.py script to produce plots

3.25/4

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 0.5

I don't have your output plots, but I took a look at your plotting code and it looks pretty good!

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, you're boxplot code isn't complete, but this looks like a good start!

Pretty plots

0/4

Exercise Points Possible Grade
Step 1.2 PC plot 1 0
Step 2.2 AFS plot 1 0
Step 3.2 Manhattan plots 1 0
Step 3.3 effect size boxplot 1 0

All of your plots are missing. Please upload them.

Grade

Total: 3.25/10

Good work! You mostly just need to upload your plots and plink commands in your README.md and you'll be good to go (other the minor plotting issues)

dtaylo95 commented 9 months ago

Regrade 12/14/2023

README.md with commands and analyses

1/2

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 0

Still missing your answer to question 3.4

plotting.py script to produce plots

3.25/4

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 0.5

The points about the manhattan plot and boxplot still stand.

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 your boxplot

Grade

Total: 7.25/10

You're getting there! Feel free to keep working on this and resubmit again.