Applied Statistical Genetics
Overheads from class
- Overheads from Introductory material (chapter 1 in the PDF text)
- Some basic R commands .txt .r for R Studio
- Overheads on more intro & Probability (chapter 2 in the PDF text)
- R commands: allele frequencies & heterozygosity .txt .r for R Studio
- R commands: Probability distributions .txt .r for R Studio
- Overheads on Hardy-Weinberg Proportions (1): Chi-squared, Likelihood Ratio, and Exact Tests
- R commands: HWP (1) .r for R Studio
- Overheads on Multinomial counts & the Delta Method
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R commands: HWP (2) .r for R Studio
R commands: genetics::genotype() .r for R Studio - Overheads on Principal Components Analysis
- R commands: population structure + PCA .r for R Studio
- R commands: for() by() & aggregate() .r for R Studio
- Overheads on Recombination and haplotypes
- Overheads on Haplotypes and the EM algorithm
- R commands: Haplotype frequency estimation & EM .r for R Studio
- Overheads on Linkage disequilibrium
- R commands: LD (1) intro .r for R Studio
- R commands: LD (2) using the genetics package .r for R Studio
- R commands: LD (3) & population structure .r for R Studio
- Overheads on the T-test & non-parametric alternative
- R commands: T-test & non-parametric alternative .r for R Studio
- Overheads on linear regression
- R commands: linear regression .r for R Studio
- *R commands: some code from the takehome .r for R Studio
- Overheads on odds ratios
- R commands: odds ratios .r for R Studio
- Overheads on logistic regression
- R commands: logistic regression .r for R Studio
- Overheads on Structure & AMOVA
- R commands: Structure & AMOVA .r for R Studio
- Overheads on Fst