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

Topics:

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

Reading:

- FAS, Chapters 15

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

Topics:

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

Reading:

- FAS, Chapters 22–28

Topics:

- Hypothesis testing
- Bayesian inference

Reading:

- FAS, Chapters 30–38

Topics:

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

Reading:

- FAS, Chapters 34–47

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

Topics:

- Principal component analysis
- Linear statistical modeling

Reading:

- FAS, Chapters 9, 54–59

Topics:

- Linear statistical modeling
- Genetic models of quantitative traits

Reading:

Topics:

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

Reading:

- FAS, Chapters 64–69

Topics:

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

Reading:

- FAS, Chapters 70–76

Optional Reading:

Topics:

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

Reading:

- FAS, Chapters 7–8, 77–79

Optional Reading:

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 |

- 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.

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) |