sim_fixed_family: Simulation with fixed family size
In FireGutter/geneference: Simulating and analysing genes with LT-FH

Description Usage Arguments Details Value Warning

Simulate genetic data, including genotypes, phenotype status and liabilities, for individuals and their family, where each individual has a fixed number of siblings specified by the sib parameter.

1	sim_fixed_family(n, m, q, hsq, k, sib = 0, path = "")

`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.
`sib`	number of siblings per individual.
`path`	directory where the files will be stored. If nothing is specified, `sim_fixed_family` writes its files in the current working directory.

Parents' genotypes are simulated and used for creating the genotypes of the individuals and their siblings. For the methodology behind the simulation, see vignette("liability-distribution").
sim_fixed_family makes use of parallel computation in order to decrease the running time. As one CPU core is left unused, the user should be able to do other work while the simulation is running.

Does not return any value, but prints the following five files to the path parameter specified in the function call:

Three text files:
- beta.txt - a file of m rows with one column. The i'th row is the true effect of the i'th SNP.
- MAFs.txt - a file of m rows with one column. The i'th row is the true Minor Allelle Frequency of the i'th SNP.
- phenotypes.txt - a file of n rows, number of columns depend on number of siblings. The file contains the phenotype status and liability of each individual as well as information on the liabilities and phenotype status of their parents and siblings.
genotypes.map - a file created such that PLINK will work with the genotype data.
genotypes.ped - the simulated genotypes in a PLINK-readable format. Note: The function only saves genotype data for the target individual.

Simulating large datasets takes time and generates large files. For details on time complexity and required disk space, see vignette("sim-benchmarks").
The largest file generated is genotypes.ped. See convert_geno_file() to convert it to another file format, thereby reducing its size significantly.

FireGutter/geneference documentation built on Dec. 17, 2021, 8:27 p.m.