validateRunSimIntegerParameters: Parameters validation for the 'runSim' function. Only integer...
In methInheritSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Description Usage Arguments Value Author(s) Examples

View source: R/methylInheritanceSimInternalMethods.R

Validation of all parameters needed by the public runSim function. Only integer parameters are validated.

1 2	validateRunSimIntegerParameters(nbSynCHR, nbSimulation, nbBlock, nbCpG, vNbSample, nbGeneration, minReads, meanCov, nbCores, vSeed)

`nbSynCHR`	a positive `integer`, the number of distinct synthetic chromosomes that will be generated.
`nbSimulation`	a positive `integer`, the number of simulations for each parameter (`vNbSample`, `vpDiff`, `vDiff` and `vInheritance`).
`nbBlock`	a positive `integer`, the number of blocks used for sampling.
`nbCpG`	a positive `integer`, the number of consecutive CpG positions used for sampling from `methInfo`.
`vNbSample`	a `vector` of positive `integer`, the number of methData (CTRL) and cases in the the simulation dataset. In the simulated dataset, the number of CTRL equals the number of Case. The number of CTRL do not need to be equal to the number of Case in the real dataset.
`nbGeneration`	a positive `integer`, the number of generations.
`minReads`	a positive `integer` Bases and regions having lower coverage than this count are discarded. The parameter correspond to the `lo.count` parameter in the `methylKit` package.
`meanCov`	a positive `integer` represent the mean of the coverage at the CpG site Default: `80`.
`nbCores`	a positive `integer`, the number of cores to use when creating the simulated datasets. Default: `1` and always `1` for Windows.
`vSeed`	a `integer`, a seed used when reproducible results are needed. When a value inferior or equal to zero is given, a random integer is used. Default: `-1`.

0 indicating that the function has been successful.

Pascal Belleau, Astrid Deschenes

## The function returns 0 when all paramaters are valid
methInheritSim:::validateRunSimIntegerParameters(nbSynCHR = 1, 
nbSimulation = 2, nbBlock = 10, nbCpG = 4, vNbSample = 10, 
nbGeneration = 3, minReads = 10, meanCov = 80, 
nbCores = 1, vSeed = -1)