Additional file 1 of On the impact of relatedness on SNP association analysis

R script for simulation. This R script supports simulation of synthetic genotypes for a family study. Instead of genotype simulation, genotypes can also be loaded from a CSV file. Allele frequencies are calculated, monomorphic SNPs are filtered and pairwise relatedness is estimated. Given SNP genotypes and a value for the heritability, variance inflation λis calculated. Additionally, the expected λ ′ is estimated. Finally, the script simulates phenotypes under the null and alternative hypothesis and provides results regarding the T statistic. The R library “mvtnorm” is required for sampling multivariate normally distributed phenotypes. Parameters can be modified to simulate different scenarios. However, the number of samples, the number of SNPs and the number of phenotype realisations per SNP should be limited to reduce the computational burden. For example, running the script on an Intel Xeon X5560 CPU (2.80 GHz) for synthetic family study 3 (SFS3) with parameter set f=111, m=2, c=3 (n=999), 100000 SNPs, 1000 phenotype realisations per SNP and 1000 SNPs required 8.3 GB RAM and took < 1 min for genotype sampling, 8 min for estimation of pairwise relatedness, 21 min for λ estimation and about 2.5 h for each of the phenotype simulations under the null and alternative hypothesis, respectively. (R 6 kb)