getting_started: Simulated Dataset for Genome-Wide Interaction Analysis

In smer: Sparse Marginal Epistasis Test

Simulated Dataset for Genome-Wide Interaction Analysis

Description

getting_started is a simulated dataset created to demonstrate the use of the sme() function for genome-wide interaction analyses. It contains results from a simulated analysis involving additive genetic effects and gene-by-gene (GxG) interactions.

Usage

data("getting_started")

Format

A list with results from sme(), including the following components:

summary

A data frame summarizing the analysis results, including p-values for SNP associations (p).

pve

A data frame containing the per SNP variance component estimates normalized to phenotypic variance explained (PVE).

vc

A data frame containing the per SNP variance component estimates.

gxg_snps

A vector containing the indices of the SNPs assigned to have epistatic interactions in the trait simulations.

Details

The dataset was generated as follows:

• Genotype Simulation: Genotype data for 5000 individuals and 6,000 SNPs was simulated with synthetic allele counts.

• Phenotype Simulation: Phenotypic values were simulated with an additive heritability of 0.3 and a GxG interaction heritability of 0.25. A set of 100 SNPs were selected for additive effects, and two groups of 5 SNPs each were used for GxG interactions.

• PLINK-Compatible Files: The simulated data was saved in PLINK-compatible .bed, .fam, and .bim files.

• Interaction Analysis: The sme() function was used to perform genome-wide interaction analyses on a subset of SNP indices, including the GxG SNP groups and 100 additional additive SNPs. Memory-efficient computation parameters (e.g., chun_ksize, n_randvecs, and n_blocks) were applied.

Key Parameters

• Additive Heritability: 0.3

• GxG Heritability: 0.25

• Number of Samples: 5000

• Number of SNPs: 6,000

• Selected Additive SNPs: 100

• Selected GxG SNP Groups:

  • Group 1: 5 SNPs

  • Group 2: 5 SNPs

Source

data-raw/getting_started.R

See Also

sme

Examples

data("getting_started")
head(getting_started$summary)

smer documentation built on April 12, 2025, 9:14 a.m.