validateRunSimOtherParameters: Parameters validation for the 'runSim' function. Only...
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 parameters other than double, integer and logical are validated.

1	validateRunSimOtherParameters(outputDir, fileID, methData, context, assembly)

`outputDir`	a string of `character` or `NULL`, the path where the files created by the function will be saved. When `NULL`, the files are saved in the current directory.
`fileID`	a string of `character`, a identifiant that will be included in each output file name. Each output file name is composed of those elements, separated by "_": a type name, ex: methylGR, methylObj, etc.. a `fileID` the chromosome number, a number between 1 and `nbSynCHR` the number of samples, a number in the `vNbSample` `vector` the mean proportion of samples that has, for a specific position, differentially methylated values, a number in the `vpDiff` `vector` the proportion of C/T for a case differentially methylated that follows a shifted beta distribution, a number in the `vDiff` `vector` the proportion of cases that inherits differentially sites, a number in the `vInheritance` `vector` the identifiant for the simulation, a number between 1 and `nbSimulation` the file extension ".rds"
`methData`	an object of class `methylBase`, the CpG information from controls (CTRL) that will be used to create the sythetic chromosome. The `methData` object can also contain information from cases but only the controls will be used.
`context`	a string of `character`, the methylation context string, ex: CpG,CpH,CHH, etc.
`assembly`	a string of `character`, the short description of the genome assembly. Ex: mm9,hg18 etc.

0 indicating that the function has been successful.

Pascal Belleau, Astrid Deschenes

## Load dataset
data("samplesForChrSynthetic")

## The function returns 0 when all paramaters are valid
methInheritSim:::validateRunSimOtherParameters(
outputDir = "test", fileID = "test", methData = samplesForChrSynthetic, 
context = "CpG", assembly = "Rnor_5.0")