Schedule

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Weekly Schedule of Topics and Reading

Week 1

Topics:

• Introduction to statistics and genomics
• Probability
• Random variables
• Genotype and allele frequencies
• Hardy-Weinberg equilibrium

Reading:

• FAS, Chapters 1–3, 10–14

Optional Reading:

• MSMGA, Chapter 1.1–1.3

Week 2

Topics:

• Joint distributions of random variables
• Hardy-Weinberg equilibrium and non-random mating

Reading:

• FAS, Chapters 15

Week 3

Topics:

• Sums of random variables
• Convergence of random variables
• Multivariate Normal and Dirichlet distributions
• Probabilistic models of RNA-seq data

Reading:

• FAS, Chapters 16–21

Week 4

Topics:

• Goals of inference
• Confidence intervals
• Hypothesis testing
• Maximum likelihood estimation

Reading:

• FAS, Chapters 22–28

Week 5

Topics:

• Hypothesis testing
• Bayesian inference

Reading:

• FAS, Chapters 30–38

Week 6

Topics:

• Bayesian estimation and classification
• Priors
• EM algorithm
• Markov chain Monte Carlo

Reading:

• FAS, Chapters 34–47

Week 7

Topics:

• Nonparametric vs parametric methods
• t distribution
• Goodness of fit
• Exact tests
• Permutation tests
• Empirical distribution functions
• Bootstrap

Reading:

• FAS, Chapters 29, 30, 48–53

Week 8

Topics:

• Principal component analysis
• Linear statistical modeling

Reading:

• FAS, Chapters 9, 54–59

Week 9

Topics:

• Linear statistical modeling
• Genetic models of quantitative traits

Reading:

• FAS, Chapters 60–63
• MSMGA, Chapters 5.1, 5.2, 6.3, 8.1–8.3

Week 10

Topics:

• Generalized linear models
• Nonparametric regression
• Generalized additive models
• Bootstrapping model fits

Reading:

• FAS, Chapters 64–69

Week 11

Topics:

• High-dimensional data and models
• Shrinkage and empirical Bayes
• False discovery rates
• Ridge regression
• Lasso regression

Reading:

• FAS, Chapters 70–76

Optional Reading:

• Stigler (1990)
• Storey and Tibshirani (2003)

Week 12

Topics:

• High-dimensional latent variable models
• Jackstraw
• Surrogate variable analysis
• Causal inference

Reading:

• FAS, Chapters 7–8, 77–79

Optional Reading:

• Chung and Storey (2014)
• Leek and Storey (2007)
• Holland (1986)

Text book abbreviations used above

Abbreviation	Full Title
AOS	All of Statistics
NPS	All of Nonparametric Statistics
DALS	Data Analysis for the Life Sciences
ESL	The Elements of Statistical Learning, 2nd Ed.
FAS	Foundations of Applied Statistics
MSMGA	Mathematical and Statistical Methods for Genetic Analysis
R4DS	R for Data Science

Notes

• AOS, NPS, and MSMGA chapter numbers refer to those in the PDF files available through Princeton University Library.
• DALS chapter titles refer to those from the Leanpub edition.
• Please obtain the most recent version of ESL from the authors’ web site.
• R4DS chapter numbers refer to those at http://r4ds.had.co.nz, NOT the printed book chapter numbers.

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Homework due dates

Assignment	Due
Homework 1	11:59PM on March 5
Homework 2	11:59PM on April 23
Scribed Notes	See syllabus
Take Home Final Exam	11:59PM on May 16 (handed out 12:00PM noon on May 13)