Heritability / Ancestry examples

Toy simulations and analyses of heritability and genetic differences

Drift and Selection

neffective_10k.R : Simulating populations a with fixed effective population size.

drift_variance.R : Visualizing variance due to drift and sampling.

allele_age.R : Visualizing the expected age of an allele.

selection_trajectory.R : Visualizing the trajectory of an allele under selection.

p_fixation.R : Visualizing the probability of fixation relative to neutral drift.

frequency_simulation.R : Visualizing the drift of alleles with/without selection.

selection_power.R : Visualizing the power to distinguish selection from drift.

polygenic_selection_simulation.R : Visualizing the allele frequency spectrum change over generations of selection.

fitness_environment.R : Visualizing a shift in the fitness optimum or environment under stabilizing selection.

breeders_eqn.R : Visualizing the response to long term selection and the Breeder's Equation.

Fst

fst_nei_hudson.R : Visualizing Nei's and Hudson's Fst.

fst_drift_migration.R : Visualizing equivalent Fst under different drift/migration parameters.

fst_ascertainment.R : Simulating Fst estimates under different SNP ascertainments.

fst_bounds.R : Sampling and visualizing the bound on Fst estimates

fst_qst.R : Visualizing the relationship between Fst and heritable trait differences

Ancestry

fst_auc_multisnp.R : Quantifying the predictive utility of genetic ancestry.

pca_vs_snps.R : Visualizing how PCA identifies two populations as more SNP data is added.

fst_phase_shift.R : Visualizing PCA sensitivity and the expected PBB threshold.

family_pca.R : Visualizing PCA run in data with family structure.

lda_structure.R : LDA/STRUCTURE model-based clustering and biases due to sampling.