sim.LDgeno.data: Generates genotypes for two genetic variants in LD

In agaye/ESPRESSO.LD: Power Analysis and Sample Size Calculation for two SNPs in Linkage Disequilibrium

Description

Generates alleles of two SNPs in LD and uses these alleles to form the genotypes of the genetic variants. Each variant can be binary or additive

Usage

sim.LDgeno.data(num.obs = 20000, MAF = c(0.1, 0.1), is.add = c(0, 0),
  r.target = 0.7, cov.mat.req)

Arguments

num.obs	Number of observations to simulate
MAF	Minor allele frequencies of the two variants
is.add	Models of the two variants
r.target	Pearson coefficient of correlation for desired level of LD
cov.mat.req	Covariance matrix required required to achieved the desired LD

Value

A dataframe that holds the genotypes and allelesdata of the two SNPs

Author(s)

Gaye A.

References

Montana, G. 2005, HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients., Bioinformatics, vol. 21 (23), pp.4309-4311.

agaye/ESPRESSO.LD documentation built on May 10, 2019, 7:31 a.m.