sim.LDsnps: Generates alleles for two biallelic SNPs in Linkage...

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

Description

Generates alleles data for pre-spcified alleles frequencies. The covariance matrix required to achieved the desired LD is computed and used to produce a random vector from a bivariate normal distribution.

Usage

sim.LDsnps(num.obs, maf.snp1 = 0.1, maf.snp2 = 0.1, r = 0.7, cov.mat.req)

Arguments

num.obs	Number of observations to simulate
maf.snp1	Minor allele frequency of the first snp
maf.snp2	Minor allele frequency of the second snp
r	Pearson coefficient of correlation for desired level of LD
cov.mat.req	Covariance matrix required required to achieved the desired LD

Value

A dataframe of two variables where the rows represent haplotypes

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.