Function reference • RyouSick

Simulation

Simulation functions that can be used to generate genotype data for a given population and related case-control phenotype data for the population with respect to a simulated target disease.

sim_disease(): Simulation of disease parameters

sim_genotypes_no_family(): Simulation of genotypes with no family

sim_genotypes_with_family(): Simulation of genotypes with family information (Fixed and non-fixed)

Analysis

Analysis functions used to infer which SNPs might be causally related to a specific disease and to find a model that can predict future cases based on an individuals genotypes.

GWAS(): Perform genome wide association study (GWAS)

GWAX(): Perform GWAS with proxy information on family case-control status (GWAX)

LTFH(): Perform GWAS on posterior mean genetic liabilities (LTFH)

Prediction_cross_validation(): Perform Prediction Cross-validation to determine best model

Predict_status(): Predict Status for new data with pre-existing model

Visualizations

Visualization functions to illustrate a basic overview of the results from analyis.

Manhattan_plot(): Make a Manhattan plot from analysis data

Power_plots(): Create power plots from GWAS, GWAX and LTFH data

Helpers

Helper functions that can be used to perform various tasks.

createRds(): Create a .rds file

OpenRds(): Open a .rds file

saveRds(): Saving the work done to an rds object

get_stats(): Get statistics on how many SNPs have been correctly identified

gibbs_sampler(): Gibbs sample posterior mean genetic liabilities

covmatrix(): Calculate co-variance matrix for liability modeling

rnorm_trunc(): Sample from a truncated normal distribution