MOJOV.simulation: Simulation for CMC.
In MOJOV: Mojo Variants: Rare Variants analysis

Provide a simulation function using ms software. If you have no ms and no Linux, you can not run this function.

MOJOV.simulation(cohortSize = 500, nReps = 2, theta = 10, sites = NULL,
affectNum = NULL, MAF = 0.01, totalMAF = 0.05, lambda = 1, sd = NULL,
type = c("alpha","belta"), sampleNum = 100, outFile = NULL, plot = FALSE, 
codeMethod = c("Proportion", "Indicator", "ChuanhuaXin"),
weightMethod = c("ChuanhuaXin"), testMethod = c("FTest", "WaldTest", 
"LRT", "Sandwich", "all"), save = NULL)

`cohortSize`	Specify the size for analysis cohort.
`nReps`	Specify the number of independent samples to generate.
`theta`	Specify the mutation parameter,see details.
`sites`	Specify the number of sites, it is optional.
`affectNum`	Specify the number or ratio for affect sites.If it is less than 1, it will be the ratio of affect rare variants sites to all rare variants.
`MAF`	Specify the minor allele frequency, and the default value is 0.01.
`totalMAF`	Specify the total minor allele frequency for affect variants. And the default value is 0.05.
`lambda`	Specify the lambda for phenotype standard error.See details.
`sd`	Specify the standard error.See details.
`type`	It can be "alpha" and "belta". The default value is "alpha".
`sampleNum`	Specify the number of sample. The default value is 100.
`outFile`	You can specify a file name to save your data from ms.
`plot`	You can set it as TRUE, it will plot the result using lattice package.
`codeMethod`	See MOJOV.analysis
`weightMethod`	See MOJOV.analysis
`testMethod`	See MOJOV.analysis
`save`	You can specify a file name to save your simulation result.