Package index • simxQTL

Genotype Simulation

Functions for simulating genotype data

sim_geno_indep(): Simulate Independent Genotypes

sim_geno_LD(): Simulate Genotypes Based on LD Matrix

sim_geno_UKB(): Simulate Genotypes Based on UK Biobank

Effect Size and Trait Simulation

Functions for simulating effect sizes and phenotypes

parse_num_causal_snps(): Parse Number of Causal SNPs

sim_beta(): Simulate QTL Effects

sim_beta_fix_variant(): Simulate Multiple Traits from Genotype and Assigned Causal Index Vector

simulate_polygenic_trait(): Simulate a Polygenic Trait

sim_multi_traits(): Simulate Multiple Traits from Genotype and Effect Sizes

Summary Statistics

Functions for simulating and calculating summary statistics

sim_sumstats(): Simulate GWAS Summary Statistics

calculate_sumstat(): Calculate Summary Statistics from Genotype and Phenotype

get_correlation(): Calculate LD (Correlation) Matrix

eQTL Simulation

Functions for simulating eQTL data

generate_eqtl_data(): Generate eQTL Data with Multiple Genetic Architecture Components

Trans-QTL Simulation

Functions for simulating trans-QTL and gene regulatory networks

simulate_cis_expression(): Simulate cis gene expression

simulate_trans_expression(): Simulate trans gene expression for different simulation scenarios

simulate_trans_mixture_celltype(): Simulate trans gene expression for a mixture of cell types

get_random_A(): Generate random adjacency matrices for trans gene associations

gene_data(): Generate gene expression data for trans-QTL analysis

gene_data_null1(): Generate null data by random shuffling of genotypes

gene_data_null2(): Generate null data by removing cis-to-trans effects

gene_data_null3(): Generate null data using ARCHIE setting

Enrichment Analysis

Functions for simulating causal enrichment

simulate_causal_config(): Simulate Causal Configuration

Utility Functions

Helper functions for calculations

compute_s2g(): Compute Genetic Variance

get_lower_chol(): Compute Lower Cholesky Decomposition