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Mar 18, 2026
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Please address issue related to sample filters
| ```{r} | ||
| # Load genotype data | ||
| geno_A1_subset <- fread("./02_activities/data/geno.A1.additive.raw") | ||
| geno_A1_subset=na.omit(geno_A1_subset) |
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This deletes samples missing genotype data for any SNP. This means it deletes samples that had non-missing values for the target SNP rs1861, but had missing values for other SNPs we aren't actually worried about. This filter step should only remove samples missing rs1861 genotypes.
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Thanks for pointing this out Eric! I have just made the change to only remove samples missing rs1861 genotypes
…ith missing values in SNP of interest
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Thanks for the quick update! Assignment complete!
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What changes are you trying to make? (e.g. Adding or removing code, refactoring existing code, adding reports)
Adding code to complete assignment 1.
What did you learn from the changes you have made?
I have learned how to use different plink commands in bash to look at .bim, .fam., and .bed files (e.g., looking at allele frequencies, calculating HWE p-values, etc). I have also learned how to do additive, recessive, and dominant coding, then evaluate associations between genotypes and phenotypes using linear regression models and visualizing it using scatterplots.
Was there another approach you were thinking about making? If so, what approach(es) were you thinking of?
N/A
Were there any challenges? If so, what issue(s) did you face? How did you overcome it?
N/A
How were these changes tested?
N/A
A reference to a related issue in your repository (if applicable)
Checklist