gsim: Genomic simulation

In psoerensen/qgg: Statistical Tools for Quantitative Genetic Analyses

Genomic simulation

Description

Simulate Genotype and Phenotype Data

Usage

gsim(Glist = NULL, chr = 1, nt = 1, W = NULL, n = 1000, m = 1000, rsids = NULL)

Arguments

Glist	A list of information about the genotype matrix. Default is 'NULL'.
chr	The chromosome(s) being used in the simulation. Default is 1.
nt	Number of traits. Default is 1.
W	Matrix of centered and scaled genotypes. Default is 'NULL'.
n	Number of individuals. Default is 1000.
m	Number of markers. Default is 1000.
rsids	A character vector of rsids. Default is 'NULL'.

Details

This function simulates genotype and phenotype data based on the 'Glist', which is information about the genotype matrix.

Value

A list containing:

• y: Phenotypes.

• W: Matrix of centered and scaled genotypes.

• e: Errors.

• g: Genotype effect.

• b0, b1: Coefficients.

• set0, set1: Selected markers.

• causal: Causal markers.

Author(s)

Peter Soerensen

Examples

## Plink bed/bim/fam files
bedfiles <- system.file("extdata", paste0("sample_chr",1:2,".bed"), package = "qgg")
bimfiles <- system.file("extdata", paste0("sample_chr",1:2,".bim"), package = "qgg")
famfiles <- system.file("extdata", paste0("sample_chr",1:2,".fam"), package = "qgg")

# Summarize bed/bim/fam files
Glist <- gprep(study="Example", bedfiles=bedfiles, bimfiles=bimfiles, famfiles=famfiles)

# Simulate phenotype
sim <- gsim(Glist=Glist, chr=1, nt=1)
head(sim$y)
head(sim$e)
head(sim$causal)

psoerensen/qgg documentation built on March 9, 2024, 10:02 p.m.