RealdataSimulation

GWAS data simulation for case-control data and quantitative traits

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1 Simulation for case-control traits

Master command
For simulation quantitative traits, it should specify --simu-qt.
For case-control data, it should specify --simu-cc and --simu-k. The --simu-cc should be followed by the number of cases and the number of controls, and --simu-k is the prevalence of the disease. It should be noted that the number of cases should not greater than k*N, in which N is the sample size in the data.

Options
--simu-seed
Specify the seed for simulation.

--simu-rep
Specify the replication for simulation. The default value is 1.

--simu-hsq
Specify the heritability for simulation. The default value is 0.5.

--simu-casual-loci
Specify the file which contains the causal SNPs.

--simu-rnd-casual-loci
Specify the number of casual loci. The default value is the number of the all loci.

--simu-order
Specify whether the effects are ordered along the genomes. It may generate correlated effects.

Example
gear --bfile test --simu-cc 500 500 --simu-k 0.01 --simu-hsq 0.8 --simu-seed 2010 --out poly
gear --bfile test --simu-cc 500 500 --simu-k 0.01 --simu-hsq 0.8 --simu-order --simu-poly-loci 100 --out poly
gear --bfile test --simu-qt 500 --simu-casual-loci 100 --simu-hsq 0.8 --out poly

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