validateRunSimIntegerParameters: Parameters validation for the 'runSim' function. Only integer...

In belleau/methylInheritanceSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Description

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

Usage

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

Arguments

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.

Value

0 indicating that the function has been successful.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## 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)

belleau/methylInheritanceSim documentation built on April 1, 2020, 2:43 p.m.