statgen-prerequisites

statgen-prerequisites#

Notes on statistical background for statistical genetics practitioners

Section	Subsection	Topic
Basic Concepts		Genotype Coding
		Minor Allele Frequency
		Hardy-Weinberg Equilibrium
Correlation	Between variants	Linkage Disequilibrium
		Linkage Disequilibrium Score
	Between individuals	Genetic Relationship Matrix
Genetic Associations	Basic model	Ordinary Least Squares
	Extend to binary outcome	Odds Ratio
	Extend to multiple variables	Marginal vs. Joint Effects
		Summary Statistics
Genetic effects		Random Effect
		Proportion of Variance Explained
		Linear Mixed Model
	Covariates	Confounder
		Collider
		Mediator
	Multiple studies	Meta Analysis Fixed Effect
		Meta Analysis Random Effect
Statistical Inference	Likelihood and MLE	Likelihood
		Maximum Likelihood Estimation
	LR and LRT	Likelihood Ratio
	Bayesian versus Frequentist	Bayesian and Frequentist
		Bayes Rule
		Bayes Factor
		P-value
	Bayesian Model	Bayesian Normal Mean Model
		Bayesian Multivariate Normal Mean Model
	Multiple Bayesian Models	Bayesian Model Comparison
		Bayesian Mixture Model