Assignment 2

[Atk1203]

What changes are you trying to make? (e.g. Adding or removing code, refactoring existing code, adding reports)

Refactored the GWAS analysis code to ensure the Manhattan plot and QQ plot render properly in the Quarto HTML output.

What did you learn from the changes you have made?

I learned that column names must exactly match what plotting functions expect; otherwise, functions like manhattan() will trigger interactive menus, which break Quarto HTML rendering.

Was there another approach you were thinking about making? If so, what approach(es) were you thinking of?

Another approach could have been to rename all columns in the original dataset at import time to standard names (CHR, BP, SNP, P) so that no further renaming is required downstream.

Were there any challenges? If so, what issue(s) did you face? How did you overcome it?

he manhattan() function kept prompting for column selections because my data column names didn’t match the defaults. Solution: I used setnames() to rename columns explicitly and passed the correct column names to the function.

How were these changes tested?

Verified that names(assoc_add) matched the required column names.
Confirmed that the QQ plot and Manhattan plot render correctly in the Quarto HTML output without interactive prompts.

A reference to a related issue in your repository (if applicable)

Checklist

I can confirm that my changes are working as intended