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eric-j-sanders
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Mar 19, 2026
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Please address interpretation of model significance.
assignment_1.qmd
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| cat("rs1861: Beta =", beta, ", p-value =", pval, "\n") | ||
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| cat ("The beta coefficient for rs1861 is approximately 0.974, indicating that each additional copy of the minor allele is associated with an increase of about 0.974 units in the phenotype under an additive model.\n") |
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In this model G=2 represents the major allele and not the minor allele, so the interpretation is not correct. (See when you calculated AF by summing genotype column, it was ~0.95 and not ~0.05)
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Thanks for the clarification! You're right, the allele coded as 2 corresponds to the major allele based on the allele frequency (~0.95). I’ve updated the interpretation accordingly in the code.
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Apr 10, 2026
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Assignment complete! But please do note my comment regarding effect interpretation.
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What changes are you trying to make? (e.g. Adding or removing code, refactoring existing code, adding reports) Completed Assignment 1 by adding the Quarto file and the rendered HTML output . Also updated file paths and moved the files to the root directory as per submission guidelines.
What did you learn from the changes you have made?
I learned how to render a Quarto document, manage file paths, and structure files correctly in a GitHub repository. I also gained experience in creating and updating pull requests.
Was there another approach you were thinking about making? If so, what approach(es) were you thinking of?
Initially, I considered keeping the files within the existing folder structure (02_activities/assignments), but later understood that the assignment required files to be in the root directory for proper evaluation.
Were there any challenges? If so, what issue(s) did you face? How did you overcome it?
Yes, I faced challenges with rendering the Quarto file and ensuring the correct file paths. I also had difficulty with the pull request setup and file placement. I overcame these issues by troubleshooting errors, rechecking instructions, and making multiple attempts.
How were these changes tested?
The changes were tested by successfully rendering the Quarto document without errors and verifying that both the .qmd and .html files are present in the root directory. I also confirmed that the pull request is accessible in an incognito window.
A reference to a related issue in your repository (if applicable)
Checklist