SimulateGWAS: Simulate GWAS data
In norment/normentR: NORMENT's Collected Plotting and Functionality Package for R

Description Usage Arguments

This function serves to simulate GWAS data. The output resembles that of the PLINK output when generated using the --assoc flag for association testing. The purpose of this function is mainly for debugging and testing of other scripts. Default setting is to create one significant column. This can be set in the AddSigSNPs field (logical). The parameters of the significant column are SigCHR to specify which chromosome the significant column should appear in (integer between 1 and 22), and the number of significant columns in nSigCols (integer). Other parameters are the number of SNPs (nSNPs) in the fake dataset, and the number of individuals in the dataset. Note that these last two parameters are subject to change due to the algorithm by which random data is generated in this function. A known bug is that the data can be a little "tail-heavy" towards the smaller chromosomes.

sim.dat <- simulateGWAS()
sim.dat <- simulateGWAS(nSNPs = 5e5, N = 2e4, 
   AddSigSNPs = FALSE, SigCHR = NULL, nSigCols = NULL)
sim.dat <- simulateGWAS(nSNPs = 2e5, N = 6e5, 
   AddSigSNPs = TRUE, SigCHR = c(2,4,6,7), nSigCols = 4)

`nSNPs`	Number of SNPs in datafile (roughly)
`N`	Number of individuals in dataset
`AddSigSNPs`	Add significant SNPs (logical)
`SigCHR`	Chromosome(s) with the significant SNPs
`nSigCols`	Number of significant columns