sim_test: Simulation directly in the R session without family history
In FireGutter/geneference: Simulating and analysing genes with LT-FH

Description Usage Arguments Details Value Warning Examples

Simulate genetic data in R, including genotypes, phenotype status and liabilities, for individuals.

1	sim_test(n, m, q, hsq, k, to_ped = T)

`n`	number of genotypes (individuals).
`m`	number of SNPS per genotype.
`q`	number of causal SNPs, i.e. SNPs that effect chances of having the phenotype.
`hsq`	squared heritability parameter.
`k`	prevalence of phenotype.
`to_ped`	if ‘TRUE', write the genotype output in PLINK’s .ped format. Else, write the number of minor alleles for each genotype at each SNP.

A quick way of simulating a small amount of data to be stored in the R-session. Note that this function only simulates data for individuals without family history, i.e. they are not simulated as offspring. Hence, the simulation cannot be used in a study of family history.

Returns a list with 5 entries, containing a matrix of genotypes, a vector specifying effect sizes of SNPs, a vector with liability of individual i, a vector specifying phenotype status of individual i, and the transformed phenotype status used for linear regression in PLINK.

Since this function saves the generated data directly in R (that is, on RAM), the function should not be used for large simulations, but rather to get an idea of the general framework.
The function does not run in parallel.