PopulationSNPSet: Simulation of a population of genotypic profiles

In fhebert/SNPSetSimulations: Simulation of genotypic profiles and binary phenotypes for GWAS

Simulation of a population of genotypic profiles

Description

PopulationSNPSet is used to generate a population matrix, where each row is a genotypic profile corresponding to an individual. It can be used to generate a matrix of genotypes according to an observed dependence structure. This function is based on the GenOrd package.

Usage

PopulationSNPSet(n, Sigma = NULL, maf = NULL, marginal = NULL,
  X = NULL)

Arguments

n	the desired number of individuals
Sigma	a correlation matrix
maf	a vector of minor allele frequencies; if this is given, Hardy-Weinberg equilibrium is assumed
marginal	a list of marginal distributions, where each element of the list is a vector of length 1 or 2 of cumulative probabilities. See the ordsample function from the GenOrd package for more information
X	an observed matrix of genotypic profiles; if this is given, the sample is simulated according to the dependence structure and marginal distributions observed in X.

Value

A matrix X of size N x p of genotypic profiles (displayed as rows).

References

Alessandro Barbiero and Pier Alda Ferrari (2015). GenOrd: Simulation of Discrete Random Variables with Given Correlation Matrix and Marginal Distributions. R package version 1.4.0. https://CRAN.R-project.org/package=GenOrd

fhebert/SNPSetSimulations documentation built on Jan. 9, 2025, 3:17 a.m.