Assignment 2_Mahin Hasan

[mahin5769]

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

Completed Assignment 2 finally (!!) including data inspection, QC, relatedness filtering, PCA, GWAS analysis, and visualization (Manhattan and QQ plots).

What did you learn from the changes you have made?

Learned how to perform GWAS analysis using PLINK2, apply quality control filters, remove related individuals, perform PCA for population stratification, and visualize results using Manhattan and QQ plots in R.

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

I considered using other tools for visualization, but qqman in R was straightforward and suitable for this assignment.

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

I faced issues with package installation (qqman) and GitHub pull request setup. I resolved them by installing the required R package and correctly configuring the repository and branches.

How were these changes tested?

The Quarto document was rendered successfully, and all outputs (HTML, plots) were generated without errors.

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

NA

Checklist

• I can confirm that my changes are working as intended

[github-actions]

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