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Notebook
A.L. Rae Centre Workshop on Genomic Prediction and Genome-Wide Association Studies
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November 9-13, 2015
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Coachman Hotel, Palmerston North, New Zealand
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Course Instructors:
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Dorian Garrick
Rohan Fernando
Topics Covered:
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Statistical, quantitative genetic, and computational aspects of genomic prediction.
Genome-wide association studies using genomic prediction methods
Julia scripts for genomic prediction and GWAS
Prerequisites:
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Graduate-level course in quantitative genetics.
Graduate-level course in statistics.
Basic understanding of concepts in QTL mapping, linkage, linkage disequilibrium and computer programming.
Notes:
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Day 1:
Introduction to Genomic Prediction
Simple Linear Models
Simulation of data using Julia
(
notebook
,
slides
)
Day 2:
Monte-Carlo Integration
Bayes' Theorem
(
notebook
,
slides
)
Introduction to MCMC Sampling
Interactive Plot of Gibbs and MH Samplers
Introduction to MCMC
Day 3:
Linear Regression Script: Inefficient
Linear Regression Script: Efficient
Linear Regression Script: Unknown Variance
Bayesian Inference
Bayesian Inference by Application to Simple Linear Regression
Bayesian Simple Linear Regression: Solutions
Pedigree-based Mixed Linear Models
Problem 1
BLUP Example
Julia Tutorial:
¶
Learn X in Y minutes
Introduction to Julia for Statistical Genetics
Package Management